Same Day VAR models predicting Coping and Self-Efficacy
Kevin Kuehn
06/08/2020
Loading packages
Reading in the data, converting data from matrix to a data frame
data<-read.csv("~/Documents/Writing/YDSP collab/YDSP/Daily data.csv")
data2<-read.spss("~/Documents/Writing/YDSP collab/YDSP/Baseline_variables.sav")## Warning in read.spss("~/Documents/Writing/YDSP collab/YDSP/
## Baseline_variables.sav"): Undeclared level(s) 3 added in variable: Ethinicitydata<-as.data.frame(data)30 variables and 952 observations. 28 observations per person, 34 people (no ID 208 and 219)
Each day, teens indicated whether or not they engaged in eight coping strategies in reference to suicidal ideation (“When you had thoughts of killing yourself in the last 24 hours, did you do any of these things to deal or cope with your thoughts?”) or, when suicidal ideation was not present, in reference to feelings or stressful events (“In the last 24 hours, did you do any of these things to deal or cope with your feelings or any stressful situations?). The eight coping behaviors included: (1) talked to a family member, (2) talked to a friend or another support person, (3) talked to a therapist, counselor, or doctor, (4) contacted a crisis line, (5) tried to distract self with something else, (6) tried to relax or do something comforting, (7) tried to tell self something calming or positive, and (8) tried a cognitive strategy that involved either (a) thinking about reasons for living (on days suicidal ideation was endorsed) or (b) thinking differently about the situation (on days when ideation was not endorsed).
For purposes of these analyses, we could only use participants who had invariant SI and/or who had enough data so that we could impute (> 50% of data).
This left us with 11 participants (11/34 = 55.88%). The following participants were used: 1 (ID = 201), 2 (ID=202), 4 (ID = 204), 5 (ID = 205), 6 (ID = 206), 7 (ID = 207), 8 (ID = 209), 10 (ID = 211), 11 (ID = 212), 13 (ID = 214), 16 (ID = 217), 18 (ID = 220), 20 (ID = 222), 21 (ID = 223), 23 (ID = 225), 24 (ID = 226), 27 (ID = 229), 28 (ID = 230), 31 (ID = 233), 34(ID=236).
Lagging each of the predictor variables for imputation
data<-slide(data=data, Var="coping_sum_3avg",TimeVar="Day",GroupVar ="ID",NewVar="coping_sum_3avg.lag",slideBy=-1)##
## Lagging coping_sum_3avg by 1 time units.## Warning: `group_by_()` is deprecated as of dplyr 0.7.0.
## Please use `group_by()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.data<-slide(data=data, Var="all_coping_talkfamily",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_talkfamily.lag",slideBy=-1)##
## Lagging all_coping_talkfamily by 1 time units.data<-slide(data=data, Var="all_coping_talkMH",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_talkMH.lag",slideBy=-1)##
## Lagging all_coping_talkMH by 1 time units.data<-slide(data=data, Var="all_coping_copingthought",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_copingthought.lag",slideBy=-1)##
## Lagging all_coping_copingthought by 1 time units.data<-slide(data=data, Var="all_coping_thinking",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_thinking.lag",slideBy=-1)##
## Lagging all_coping_thinking by 1 time units.data<-slide(data=data, Var="all_coping_talkfriend",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_talkfriend.lag",slideBy=-1)##
## Lagging all_coping_talkfriend by 1 time units.data<-slide(data=data, Var="all_coping_dis_rel_combined",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_dis_rel_combined.lag",slideBy=-1)##
## Lagging all_coping_dis_rel_combined by 1 time units.data<-slide(data=data, Var="all_coping_crisisline",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_crisisline.lag",slideBy=-1)##
## Lagging all_coping_crisisline by 1 time units.data<-slide(data=data, Var="coping_sum",TimeVar="Day",GroupVar ="ID",NewVar="coping_sum.lag",slideBy=-1)##
## Lagging coping_sum by 1 time units.data<-slide(data=data, Var="all_coping_any",TimeVar="Day",GroupVar ="ID",NewVar="all_coping_any.lag",slideBy=-1)##
## Lagging all_coping_any by 1 time units.data<-slide(data=data, Var="SIUrge",TimeVar="Day",GroupVar ="ID",NewVar="SIUrge.lag",slideBy=-1)##
## Lagging SIUrge by 1 time units.data<-slide(data=data, Var="Self_Efficacy",TimeVar="Day",GroupVar ="ID",NewVar="Self_Efficacy.lag",slideBy=-1)##
## Lagging Self_Efficacy by 1 time units.Splitting the data into individual data files based on ID
pdat_split <- split(data, data$ID)
new_names<-as.character(c(unique(data$ID)))
for(i in seq_along(pdat_split)){
new_names[i] <- paste0("pdat", i, sep="")
}
for (i in 1:length(pdat_split)) {
assign(new_names[i], pdat_split[[i]])
}Person 202
Specifying the data structure for imputation
MImodel = pdat2[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 311k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(as.factor(data.impute[,1]))
all_coping_talkMH.imp = as.factor(as.factor(data.impute[,2]))
all_coping_copingthought.imp = as.factor(as.factor(data.impute[,3]))
all_coping_thinking.imp = as.factor(as.factor(data.impute[,4]))
all_coping_talkfriend.imp = as.factor(as.factor(data.impute[,5]))
all_coping_dis_rel_combined.imp = as.factor(as.factor(data.impute[,6]))
all_coping_crisisline.imp = as.factor(as.factor(data.impute[,7]))
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(as.factor(data.impute[,10]))
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat2.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp =all_coping_talkMH.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat2.1<-pdat2.imp[vars]
pdat2.2<- do.call(rbind, apply(pdat2.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat2.3<-pdat2.imp[vars]
pdat2.4 <- do.call(rbind, apply(pdat2.3, 1, function(x) {rbind(na.df, x)}))
pdat2.imp<-cbind(pdat2.4, pdat2.2)
pdat2.imp$Day<-c(1:56)Creating splines
pdat2.imp<-data.frame(na.spline(pdat2.imp))
pdat2.imp<-round(pdat2.imp)
pdat2.imp$SIUrge.imp[pdat2.imp$SIUrge.imp>7]<-7
pdat2.imp$SIUrge.imp[pdat2.imp$SIUrge.imp<0]<-0
pdat2.imp$Self_Efficacy.imp[pdat2.imp$Self_Efficacy.imp>10]<-10
pdat2.imp$Self_Efficacy.imp[pdat2.imp$Self_Efficacy.imp<0]<-0
pdat2.imp$all_coping_talkMH.imp[pdat2.imp$all_coping_talkMH.imp==-2]<-0cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat2.imp <- pdat2.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
pdat2.imp[cols] <- lapply(pdat2.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat2, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat2.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting Residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat2.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod4<-glm(all_coping_any.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_any_resid<-as.numeric(rstandard(mod4))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat2.imp, na.action=na.exclude)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat2.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat2.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat2.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat2<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_any_resid, Coping_sum_3avg_resid))Calculating difference scores
attach(pdat2)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_any_resid = diff(Coping_any_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid=diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat2<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_sum_3avg_resid))
pdat2$day<-c(1:55)Same Day models with SI Urge predicting changes in coping
pdat2.2<-c("SIUrge_resid", "Coping_sum_3avg_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 0.056427, df1 = 1, df2 = 102, p-value = 0.8127summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: SIUrge_resid, Coping_sum_3avg_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -95.085
## Roots of the characteristic polynomial:
## 0.5055 0.05981
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = SIUrge_resid.l1 + Coping_sum_3avg_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## SIUrge_resid.l1 0.504926 0.123644 4.084 0.000157 ***
## Coping_sum_3avg_resid.l1 -0.015048 0.200297 -0.075 0.940407
## const -0.004476 0.099857 -0.045 0.964423
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7328 on 51 degrees of freedom
## Multiple R-Squared: 0.2475, Adjusted R-squared: 0.218
## F-statistic: 8.389 on 2 and 51 DF, p-value: 0.0007086
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = SIUrge_resid.l1 + Coping_sum_3avg_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## SIUrge_resid.l1 -0.01990 0.08379 -0.238 0.813
## Coping_sum_3avg_resid.l1 -0.05928 0.13574 -0.437 0.664
## const -0.03542 0.06767 -0.523 0.603
##
##
## Residual standard error: 0.4966 on 51 degrees of freedom
## Multiple R-Squared: 0.005256, Adjusted R-squared: -0.03375
## F-statistic: 0.1347 on 2 and 51 DF, p-value: 0.8743
##
##
##
## Covariance matrix of residuals:
## SIUrge_resid Coping_sum_3avg_resid
## SIUrge_resid 0.5370 0.0489
## Coping_sum_3avg_resid 0.0489 0.2466
##
## Correlation matrix of residuals:
## SIUrge_resid Coping_sum_3avg_resid
## SIUrge_resid 1.0000 0.1344
## Coping_sum_3avg_resid 0.1344 1.0000pdat2.2<-c("SIUrge_resid", "Coping_TalkFamily_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 5.3662, df1 = 1, df2 = 102, p-value = 0.02253summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: SIUrge_resid, Coping_TalkFamily_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -128.081
## Roots of the characteristic polynomial:
## 0.3678 0.113
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = SIUrge_resid.l1 + Coping_TalkFamily_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## SIUrge_resid.l1 0.56572 0.12160 4.652 2.36e-05 ***
## Coping_TalkFamily_resid.l1 -0.23637 0.11198 -2.111 0.0397 *
## const -0.01067 0.09574 -0.111 0.9117
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7028 on 51 degrees of freedom
## Multiple R-Squared: 0.3079, Adjusted R-squared: 0.2808
## F-statistic: 11.34 on 2 and 51 DF, p-value: 8.397e-05
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = SIUrge_resid.l1 + Coping_TalkFamily_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## SIUrge_resid.l1 0.37902 0.16362 2.317 0.0246 *
## Coping_TalkFamily_resid.l1 -0.08488 0.15068 -0.563 0.5757
## const 0.02154 0.12882 0.167 0.8679
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9456 on 51 degrees of freedom
## Multiple R-Squared: 0.0952, Adjusted R-squared: 0.05972
## F-statistic: 2.683 on 2 and 51 DF, p-value: 0.07799
##
##
##
## Covariance matrix of residuals:
## SIUrge_resid Coping_TalkFamily_resid
## SIUrge_resid 0.49392 -0.01508
## Coping_TalkFamily_resid -0.01508 0.89424
##
## Correlation matrix of residuals:
## SIUrge_resid Coping_TalkFamily_resid
## SIUrge_resid 1.00000 -0.02269
## Coping_TalkFamily_resid -0.02269 1.00000pdat2.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 13.601, df1 = 1, df2 = 102, p-value = 0.0003646summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -129.076
## Roots of the characteristic polynomial:
## 0.2617 0.1802
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.18880 0.13436 -1.405 0.166045
## SIUrge_resid.l1 0.66799 0.18113 3.688 0.000549 ***
## const 0.02422 0.13600 0.178 0.859340
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9986 on 51 degrees of freedom
## Multiple R-Squared: 0.2105, Adjusted R-squared: 0.1796
## F-statistic: 6.8 on 2 and 51 DF, p-value: 0.00241
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.248863 0.092241 -2.698 0.00943 **
## SIUrge_resid.l1 0.630714 0.124346 5.072 5.56e-06 ***
## const 0.001254 0.093367 0.013 0.98933
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6856 on 51 degrees of freedom
## Multiple R-Squared: 0.3414, Adjusted R-squared: 0.3156
## F-statistic: 13.22 on 2 and 51 DF, p-value: 2.366e-05
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 0.9973 0.1034
## SIUrge_resid 0.1034 0.4700
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.000 0.151
## SIUrge_resid 0.151 1.000pdat2.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 0.19811, df1 = 1, df2 = 102, p-value = 0.6572summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -129.748
## Roots of the characteristic polynomial:
## 0.5045 0.00955
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.008065 0.140296 -0.057 0.954
## SIUrge_resid.l1 -0.070328 0.158007 -0.445 0.658
## const -0.041691 0.127731 -0.326 0.745
##
##
## Residual standard error: 0.9372 on 51 degrees of freedom
## Multiple R-Squared: 0.003876, Adjusted R-squared: -0.03519
## F-statistic: 0.09923 on 2 and 51 DF, p-value: 0.9057
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.010822 0.109699 -0.099 0.921798
## SIUrge_resid.l1 0.502970 0.123547 4.071 0.000163 ***
## const -0.004618 0.099874 -0.046 0.963301
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7328 on 51 degrees of freedom
## Multiple R-Squared: 0.2476, Adjusted R-squared: 0.2181
## F-statistic: 8.391 on 2 and 51 DF, p-value: 0.0007072
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 0.87828 -0.04515
## SIUrge_resid -0.04515 0.53697
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 -0.06575
## SIUrge_resid -0.06575 1.00000pdat2.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 1.7513, df1 = 1, df2 = 102, p-value = 0.1887summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -127.459
## Roots of the characteristic polynomial:
## 0.495 0.01052
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.03819 0.13156 -0.290 0.773
## SIUrge_resid.l1 -0.20802 0.15719 -1.323 0.192
## const 0.05322 0.12432 0.428 0.670
##
##
## Residual standard error: 0.913 on 51 degrees of freedom
## Multiple R-Squared: 0.0332, Adjusted R-squared: -0.004715
## F-statistic: 0.8756 on 2 and 51 DF, p-value: 0.4228
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.070943 0.105128 0.675 0.502836
## SIUrge_resid.l1 0.522673 0.125611 4.161 0.000122 ***
## const -0.004702 0.099345 -0.047 0.962438
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7296 on 51 degrees of freedom
## Multiple R-Squared: 0.2541, Adjusted R-squared: 0.2249
## F-statistic: 8.687 on 2 and 51 DF, p-value: 0.0005665
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 0.8336 -0.1112
## SIUrge_resid -0.1112 0.5323
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.000 -0.167
## SIUrge_resid -0.167 1.000pdat2.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 0.60949, df1 = 1, df2 = 102, p-value = 0.4368summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -130.744
## Roots of the characteristic polynomial:
## 0.5072 0.03105
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.03767 0.14647 -0.257 0.798
## SIUrge_resid.l1 -0.13771 0.17639 -0.781 0.439
## const -0.04034 0.13598 -0.297 0.768
##
##
## Residual standard error: 0.9981 on 51 degrees of freedom
## Multiple R-Squared: 0.01181, Adjusted R-squared: -0.02694
## F-statistic: 0.3049 on 2 and 51 DF, p-value: 0.7386
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.026213 0.107490 0.244 0.808316
## SIUrge_resid.l1 0.513863 0.129442 3.970 0.000226 ***
## const -0.003333 0.099787 -0.033 0.973486
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7324 on 51 degrees of freedom
## Multiple R-Squared: 0.2483, Adjusted R-squared: 0.2189
## F-statistic: 8.424 on 2 and 51 DF, p-value: 0.0006898
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.9961 -0.2171
## SIUrge_resid -0.2171 0.5364
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.000 -0.297
## SIUrge_resid -0.297 1.000pdat2.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 6.981, df1 = 1, df2 = 102, p-value = 0.009536summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -136.184
## Roots of the characteristic polynomial:
## 0.2873 0.2049
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.04461 0.12711 -0.351 0.7271
## SIUrge_resid.l1 0.49178 0.18613 2.642 0.0109 *
## const -0.02704 0.14959 -0.181 0.8573
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.098 on 51 degrees of freedom
## Multiple R-Squared: 0.1204, Adjusted R-squared: 0.08591
## F-statistic: 3.491 on 2 and 51 DF, p-value: 0.03795
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.1683819 0.0814643 -2.067 0.0438 *
## SIUrge_resid.l1 0.5367775 0.1192875 4.500 3.96e-05 ***
## const 0.0001333 0.0958731 0.001 0.9989
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.704 on 51 degrees of freedom
## Multiple R-Squared: 0.3056, Adjusted R-squared: 0.2784
## F-statistic: 11.22 on 2 and 51 DF, p-value: 9.136e-05
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.20648 -0.04384
## SIUrge_resid -0.04384 0.49556
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.0000 -0.0567
## SIUrge_resid -0.0567 1.0000pdat2.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 15.3, df1 = 1, df2 = 102, p-value = 0.0001655summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -100.305
## Roots of the characteristic polynomial:
## 0.516 0.516
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.11970 0.12602 0.950 0.346692
## SIUrge_resid.l1 0.43134 0.11028 3.911 0.000272 ***
## const -0.02161 0.08317 -0.260 0.796090
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6108 on 51 degrees of freedom
## Multiple R-Squared: 0.3002, Adjusted R-squared: 0.2727
## F-statistic: 10.94 on 2 and 51 DF, p-value: 0.0001114
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 -0.4383594 0.1381972 -3.172 0.00256 **
## SIUrge_resid.l1 0.6448324 0.1209277 5.332 2.23e-06 ***
## const 0.0008683 0.0912074 0.010 0.99244
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6698 on 51 degrees of freedom
## Multiple R-Squared: 0.3715, Adjusted R-squared: 0.3468
## F-statistic: 15.07 on 2 and 51 DF, p-value: 7.205e-06
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.37303 0.09762
## SIUrge_resid 0.09762 0.44857
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.0000 0.2386
## SIUrge_resid 0.2386 1.0000pdat2.2<-c("Efficacy_resid", "SIUrge_resid")
pdat2.2<-pdat2[pdat2.2]
coping_var=VAR(pdat2.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 5.7675, df1 = 1, df2 = 102, p-value = 0.01814summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -112.45
## Roots of the characteristic polynomial:
## 0.6057 0.6057
## Call:
## VAR(y = pdat2.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.57141 0.14084 4.057 0.000171 ***
## SIUrge_resid.l1 0.30542 0.12718 2.402 0.020008 *
## const -0.04533 0.10113 -0.448 0.655893
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7408 on 51 degrees of freedom
## Multiple R-Squared: 0.2715, Adjusted R-squared: 0.2429
## F-statistic: 9.504 on 2 and 51 DF, p-value: 0.0003104
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 -0.39734 0.12774 -3.111 0.003055 **
## SIUrge_resid.l1 0.42976 0.11534 3.726 0.000488 ***
## const 0.01620 0.09172 0.177 0.860495
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6719 on 51 degrees of freedom
## Multiple R-Squared: 0.3675, Adjusted R-squared: 0.3427
## F-statistic: 14.81 on 2 and 51 DF, p-value: 8.468e-06
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.54879 -0.01753
## SIUrge_resid -0.01753 0.45142
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.00000 -0.03522
## SIUrge_resid -0.03522 1.00000Plotting Self-Efficacy and SI Urge over time
df <- pdat2.imp %>%
dplyr::select(Day, SIUrge.imp, Self_Efficacy.imp) %>%
tidyr::gather(key = "variable", value = "value", -Day)
a<-ggplot(df, aes(x = Day, y = value)) +
geom_line(aes(color = variable), size = 1) +
scale_color_manual(values = c("#00AFBB", "#E7B800"), name="Variable", labels=c("Efficacy", "Suicidal Urge")) + labs(y="Value") +
theme_minimal()Person 204
Specifying Data Structure
MImodel = pdat4[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## * Please inspect the loggedEvents## Warning: Number of logged events: 562k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat4.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp =all_coping_talkMH.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructing to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat4.1<-pdat4.imp[vars]
pdat4.2<- do.call(rbind, apply(pdat4.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat4.3<-pdat4.imp[vars]
pdat4.4 <- do.call(rbind, apply(pdat4.3, 1, function(x) {rbind(na.df, x)}))
pdat4.imp<-cbind(pdat4.4, pdat4.2)
pdat4.imp$Day<-c(1:56)Creating splines
pdat4.imp<-data.frame(na.spline(pdat4.imp))
pdat4.imp<-round(pdat4.imp)
pdat4.imp$SIUrge.imp[pdat4.imp$SIUrge.imp>7]<-7
pdat4.imp$SIUrge.imp[pdat4.imp$SIUrge.imp<0]<-0
pdat4.imp$Self_Efficacy.imp[pdat4.imp$Self_Efficacy.imp>10]<-10
pdat4.imp$Self_Efficacy.imp[pdat4.imp$Self_Efficacy.imp<0]<-0cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat4.imp <- pdat4.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
pdat4.imp[cols] <- lapply(pdat4.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat4, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat4.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting Residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat4.imp)
Coping_sum_3avg_resid=rstandard(mod1)
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod4<-glm(all_coping_any.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_any_resid<-as.numeric(rstandard(mod4))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat4.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat4.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat4.imp, na.action=na.exclude)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat4.imp, na.action=na.exclude)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat4<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_sum_3avg_resid))Calculating Difference Scores
attach(pdat4)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat2:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_any_resid = diff(Coping_any_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat4<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_sum_3avg_resid))
pdat4$day<-c(1:55)Same Day models with SI Urge Predicting Changes in Coping
pdat4.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 0.00038425, df1 = 1, df2 = 102, p-value = 0.9844summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -74.337
## Roots of the characteristic polynomial:
## 0.4081 0.06836
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.06779 0.13460 0.504 0.617
## SIUrge_resid.l1 -0.00184 0.09389 -0.020 0.984
## const -0.01061 0.05810 -0.183 0.856
##
##
## Residual standard error: 0.4258 on 51 degrees of freedom
## Multiple R-Squared: 0.00495, Adjusted R-squared: -0.03407
## F-statistic: 0.1268 on 2 and 51 DF, p-value: 0.8812
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.104907 0.182510 0.575 0.5680
## SIUrge_resid.l1 0.408697 0.127313 3.210 0.0023 **
## const -0.008395 0.078788 -0.107 0.9156
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5774 on 51 degrees of freedom
## Multiple R-Squared: 0.1753, Adjusted R-squared: 0.1429
## F-statistic: 5.419 on 2 and 51 DF, p-value: 0.007349
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.18133 0.01203
## SIUrge_resid 0.01203 0.33340
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.00000 0.04891
## SIUrge_resid 0.04891 1.00000pdat4.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 1.0806e-08, df1 = 1, df2 = 102, p-value = 0.9999summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -105.794
## Roots of the characteristic polynomial:
## 0.4122 0.003782
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -3.787e-03 1.400e-01 -0.027 0.979
## SIUrge_resid.l1 -1.762e-05 1.695e-01 0.000 1.000
## const -3.932e-02 1.050e-01 -0.375 0.709
##
##
## Residual standard error: 0.7698 on 51 degrees of freedom
## Multiple R-Squared: 1.434e-05, Adjusted R-squared: -0.0392
## F-statistic: 0.0003658 on 2 and 51 DF, p-value: 0.9996
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.124929 0.103908 1.202 0.23480
## SIUrge_resid.l1 0.412199 0.125808 3.276 0.00189 **
## const -0.006504 0.077880 -0.084 0.93377
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5712 on 51 degrees of freedom
## Multiple R-Squared: 0.1928, Adjusted R-squared: 0.1611
## F-statistic: 6.09 on 2 and 51 DF, p-value: 0.004248
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 0.592600 0.000281
## SIUrge_resid 0.000281 0.326314
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.0000000 0.0006391
## SIUrge_resid 0.0006391 1.0000000pdat4.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 4.1646, df1 = 1, df2 = 102, p-value = 0.04386summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -109.738
## Roots of the characteristic polynomial:
## 0.3454 0.05453
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.018974 0.134960 -0.141 0.8887
## SIUrge_resid.l1 0.370526 0.181566 2.041 0.0465 *
## const -0.004304 0.111983 -0.038 0.9695
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8224 on 51 degrees of freedom
## Multiple R-Squared: 0.07549, Adjusted R-squared: 0.03924
## F-statistic: 2.082 on 2 and 51 DF, p-value: 0.1351
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.07228 0.09452 -0.765 0.4479
## SIUrge_resid.l1 0.41890 0.12716 3.294 0.0018 **
## const -0.01209 0.07843 -0.154 0.8781
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.576 on 51 degrees of freedom
## Multiple R-Squared: 0.1793, Adjusted R-squared: 0.1471
## F-statistic: 5.572 on 2 and 51 DF, p-value: 0.006478
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 0.67642 -0.02496
## SIUrge_resid -0.02496 0.33176
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.00000 -0.05268
## SIUrge_resid -0.05268 1.00000pdat4.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 3.4565e-07, df1 = 1, df2 = 102, p-value = 0.9995summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -115.418
## Roots of the characteristic polynomial:
## 0.4122 0.002746
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.0027459 0.1400278 -0.020 0.984
## SIUrge_resid.l1 -0.0001175 0.1998024 -0.001 1.000
## const -0.0352553 0.1236149 -0.285 0.777
##
##
## Residual standard error: 0.9072 on 51 degrees of freedom
## Multiple R-Squared: 7.547e-06, Adjusted R-squared: -0.03921
## F-statistic: 0.0001924 on 2 and 51 DF, p-value: 0.9998
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -2.299e-05 8.941e-02 0.000 0.99980
## SIUrge_resid.l1 4.122e-01 1.276e-01 3.231 0.00216 **
## const -1.140e-02 7.893e-02 -0.144 0.88574
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5793 on 51 degrees of freedom
## Multiple R-Squared: 0.1699, Adjusted R-squared: 0.1374
## F-statistic: 5.219 on 2 and 51 DF, p-value: 0.008664
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 8.23e-01 -0.0000231
## SIUrge_resid -2.31e-05 0.3355628
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.000e+00 -4.395e-05
## SIUrge_resid -4.395e-05 1.000e+00pdat4.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 5.1684e-07, df1 = 1, df2 = 102, p-value = 0.9994summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -100.755
## Roots of the characteristic polynomial:
## 0.4122 0.0002698
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.0002698 0.1400280 0.002 0.998
## SIUrge_resid.l1 -0.0001095 0.1522905 -0.001 0.999
## const 0.0060110 0.0941486 0.064 0.949
##
##
## Residual standard error: 0.6915 on 51 degrees of freedom
## Multiple R-Squared: 8.294e-08, Adjusted R-squared: -0.03922
## F-statistic: 2.115e-06 on 2 and 51 DF, p-value: 1
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -8.115e-05 1.173e-01 -0.001 0.99945
## SIUrge_resid.l1 4.122e-01 1.276e-01 3.231 0.00216 **
## const -1.140e-02 7.887e-02 -0.145 0.88566
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5793 on 51 degrees of freedom
## Multiple R-Squared: 0.1699, Adjusted R-squared: 0.1374
## F-statistic: 5.219 on 2 and 51 DF, p-value: 0.008664
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 4.781e-01 -3.408e-05
## SIUrge_resid -3.408e-05 3.356e-01
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.000e+00 -8.508e-05
## SIUrge_resid -8.508e-05 1.000e+00pdat4.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 2.5552, df1 = 1, df2 = 102, p-value = 0.113summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -120.776
## Roots of the characteristic polynomial:
## 0.4561 0.1347
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.048506 0.139989 -0.346 0.730
## SIUrge_resid.l1 0.374177 0.234081 1.598 0.116
## const 0.008865 0.141257 0.063 0.950
##
##
## Residual standard error: 1.037 on 51 degrees of freedom
## Multiple R-Squared: 0.04771, Adjusted R-squared: 0.01037
## F-statistic: 1.278 on 2 and 51 DF, p-value: 0.2875
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.11619 0.07645 1.520 0.13474
## SIUrge_resid.l1 0.37000 0.12784 2.894 0.00558 **
## const -0.01238 0.07714 -0.161 0.87309
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5666 on 51 degrees of freedom
## Multiple R-Squared: 0.2059, Adjusted R-squared: 0.1747
## F-statistic: 6.611 on 2 and 51 DF, p-value: 0.0028
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.07637 0.09348
## SIUrge_resid 0.09348 0.32102
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.000 0.159
## SIUrge_resid 0.159 1.000pdat4.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 0.18073, df1 = 1, df2 = 102, p-value = 0.6716summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -118.432
## Roots of the characteristic polynomial:
## 0.4247 0.02478
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.003375 0.140013 -0.024 0.981
## SIUrge_resid.l1 0.091337 0.214851 0.425 0.673
## const -0.009220 0.132606 -0.070 0.945
##
##
## Residual standard error: 0.9739 on 51 degrees of freedom
## Multiple R-Squared: 0.003531, Adjusted R-squared: -0.03555
## F-statistic: 0.09036 on 2 and 51 DF, p-value: 0.9137
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.10032 0.08208 1.222 0.22726
## SIUrge_resid.l1 0.40333 0.12596 3.202 0.00235 **
## const -0.01046 0.07774 -0.135 0.89348
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.571 on 51 degrees of freedom
## Multiple R-Squared: 0.1935, Adjusted R-squared: 0.1619
## F-statistic: 6.119 on 2 and 51 DF, p-value: 0.00415
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 0.94853 0.02087
## SIUrge_resid 0.02087 0.32601
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 0.03753
## SIUrge_resid 0.03753 1.00000pdat4.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 0.37762, df1 = 1, df2 = 102, p-value = 0.5402summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -85.707
## Roots of the characteristic polynomial:
## 0.4432 0.2813
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.322209 0.120231 2.680 0.00989 **
## SIUrge_resid.l1 0.072159 0.117426 0.615 0.54161
## const 0.006969 0.072163 0.097 0.92344
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5273 on 51 degrees of freedom
## Multiple R-Squared: 0.1389, Adjusted R-squared: 0.1051
## F-statistic: 4.114 on 2 and 51 DF, p-value: 0.02207
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.068560 0.131731 0.520 0.60500
## SIUrge_resid.l1 0.402289 0.128658 3.127 0.00292 **
## const -0.007232 0.079066 -0.091 0.92748
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5777 on 51 degrees of freedom
## Multiple R-Squared: 0.1743, Adjusted R-squared: 0.1419
## F-statistic: 5.383 on 2 and 51 DF, p-value: 0.007569
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.27805 0.03029
## SIUrge_resid 0.03029 0.33379
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.00000 0.09942
## SIUrge_resid 0.09942 1.00000pdat4.2<-c("Efficacy_resid", "SIUrge_resid")
pdat4.2<-pdat4[pdat4.2]
coping_var=VAR(pdat4.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 3.2332, df1 = 1, df2 = 102, p-value = 0.07512summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -90.95
## Roots of the characteristic polynomial:
## 0.3673 0.3673
## Call:
## VAR(y = pdat4.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.24033 0.15575 1.543 0.1290
## SIUrge_resid.l1 -0.23866 0.13273 -1.798 0.0781 .
## const 0.03049 0.07969 0.383 0.7036
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5852 on 51 degrees of freedom
## Multiple R-Squared: 0.1262, Adjusted R-squared: 0.09189
## F-statistic: 3.682 on 2 and 51 DF, p-value: 0.0321
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.124509 0.153201 0.813 0.42016
## SIUrge_resid.l1 0.437586 0.130552 3.352 0.00152 **
## const -0.009992 0.078382 -0.127 0.89906
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5756 on 51 degrees of freedom
## Multiple R-Squared: 0.1805, Adjusted R-squared: 0.1484
## F-statistic: 5.617 on 2 and 51 DF, p-value: 0.00624
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.34240 -0.04286
## SIUrge_resid -0.04286 0.33127
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 -0.1273
## SIUrge_resid -0.1273 1.0000Plotting SI Urge and the 3 day coping diversity variable over time
df <- pdat4.imp %>%
dplyr::select(Day, SIUrge.imp, coping_sum_3avg.imp) %>%
tidyr::gather(key = "variable", value = "value", -Day)
ggplot(df, aes(x = Day, y = value)) +
geom_line(aes(color = variable), size = 1) +
scale_color_manual(values = c("#00AFBB", "#E7B800")) +
theme_minimal()
205
Specifying the data structure
MImodel = pdat5[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_talkfriend coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 223k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat5.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp =all_coping_talkMH.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp,
all_coping_any.imp = all_coping_any.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat5.1<-pdat5.imp[vars]
pdat5.2<- do.call(rbind, apply(pdat5.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat5.3<-pdat5.imp[vars]
pdat5.4 <- do.call(rbind, apply(pdat5.3, 1, function(x) {rbind(na.df, x)}))
pdat5.imp<-cbind(pdat5.4, pdat5.2)
pdat5.imp$Day<-c(1:56)Creating splines
pdat5.imp<-data.frame(na.spline(pdat5.imp))
pdat5.imp<-round(pdat5.imp)
pdat5.imp$SIUrge.imp[pdat5.imp$SIUrge.imp>7]<-7
pdat5.imp$SIUrge.imp[pdat5.imp$SIUrge.imp<0]<-0
pdat5.imp$Self_Efficacy.imp[pdat5.imp$Self_Efficacy.imp>10]<-10
pdat5.imp$Self_Efficacy.imp[pdat5.imp$Self_Efficacy.imp<0]<-0pdat5.imp <- pdat5.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat5.imp[cols] <- lapply(pdat5.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat5, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat5.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat5.imp)
Coping_sum_3avg_resid=as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat5.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat5.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod4<-glm(all_coping_any.imp~Day, data=pdat5.imp, family=binomial(link="logit"))
Coping_any_resid<-as.numeric(rstandard(mod4))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat5.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod8<-lm(coping_sum.imp~Day, data=pdat5.imp, na.action=na.exclude)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat5.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat5.imp, na.action=na.exclude)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat5.imp, na.action=na.exclude)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat5<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_any_resid, Coping_sum_3avg_resid))## Warning in base::cbind(...): number of rows of result is not a multiple of
## vector length (arg 4)Person 5: Calculating Difference Scores
attach(pdat5)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_any_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat4:
##
## Coping_sum_3avg_resid, Coping_sum_resid, Coping_TalkFamily_resid,
## Coping_TalkFriend_resid, Coping_TalkMH_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_resid## The following objects are masked from pdat2:
##
## Coping_any_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_any_resid = diff(Coping_any_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat5<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, Efficacy_resid, SIUrge_resid, Coping_sum_3avg_resid))## Warning in base::cbind(...): number of rows of result is not a multiple of
## vector length (arg 4)pdat5$day<-c(1:55)Person 5: Same Days models with SI Urge Predicting Changes in Coping
pdat5.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat5.2<-pdat5[pdat5.2]
coping_var=VAR(pdat5.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 1.7464, df1 = 1, df2 = 102, p-value = 0.1893summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -130.043
## Roots of the characteristic polynomial:
## 0.4872 0.02983
## Call:
## VAR(y = pdat5.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.01507 0.13806 -0.109 0.914
## SIUrge_resid.l1 -0.28841 0.21824 -1.322 0.192
## const -0.03044 0.15142 -0.201 0.841
##
##
## Residual standard error: 1.112 on 51 degrees of freedom
## Multiple R-Squared: 0.03311, Adjusted R-squared: -0.004804
## F-statistic: 0.8733 on 2 and 51 DF, p-value: 0.4237
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.02570 0.07689 -0.334 0.739526
## SIUrge_resid.l1 0.47247 0.12154 3.887 0.000294 ***
## const -0.01007 0.08433 -0.119 0.905390
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6195 on 51 degrees of freedom
## Multiple R-Squared: 0.233, Adjusted R-squared: 0.2029
## F-statistic: 7.747 on 2 and 51 DF, p-value: 0.001154
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.237286 0.009802
## SIUrge_resid 0.009802 0.383756
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.00000 0.01422
## SIUrge_resid 0.01422 1.00000pdat5.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat5.2<-pdat5[pdat5.2]
coping_var=VAR(pdat5.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 1.6117, df1 = 1, df2 = 102, p-value = 0.2071summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -125.117
## Roots of the characteristic polynomial:
## 0.4554 0.008791
## Call:
## VAR(y = pdat5.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.01751 0.13841 -0.127 0.900
## SIUrge_resid.l1 0.25376 0.19989 1.270 0.210
## const -0.04501 0.13860 -0.325 0.747
##
##
## Residual standard error: 1.018 on 51 degrees of freedom
## Multiple R-Squared: 0.03064, Adjusted R-squared: -0.007376
## F-statistic: 0.806 on 2 and 51 DF, p-value: 0.4523
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.04902 0.08408 -0.583 0.562439
## SIUrge_resid.l1 0.48167 0.12142 3.967 0.000228 ***
## const -0.01149 0.08420 -0.136 0.891967
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6181 on 51 degrees of freedom
## Multiple R-Squared: 0.2364, Adjusted R-squared: 0.2065
## F-statistic: 7.896 on 2 and 51 DF, p-value: 0.00103
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.035353 0.002716
## SIUrge_resid 0.002716 0.382050
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.000000 0.004319
## SIUrge_resid 0.004319 1.000000pdat5.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat5.2<-pdat5[pdat5.2]
coping_var=VAR(pdat5.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 0.66997, df1 = 1, df2 = 102, p-value = 0.415summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -114.664
## Roots of the characteristic polynomial:
## 0.4383 0.04988
## Call:
## VAR(y = pdat5.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.03118 0.14523 0.215 0.831
## SIUrge_resid.l1 0.15242 0.18622 0.819 0.417
## const -0.01978 0.12409 -0.159 0.874
##
##
## Residual standard error: 0.9116 on 51 degrees of freedom
## Multiple R-Squared: 0.01297, Adjusted R-squared: -0.02573
## F-statistic: 0.3352 on 2 and 51 DF, p-value: 0.7168
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.04994 0.09856 -0.507 0.614544
## SIUrge_resid.l1 0.45704 0.12637 3.617 0.000684 ***
## const -0.01036 0.08421 -0.123 0.902555
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6186 on 51 degrees of freedom
## Multiple R-Squared: 0.2352, Adjusted R-squared: 0.2052
## F-statistic: 7.841 on 2 and 51 DF, p-value: 0.001073
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 0.8309 -0.2222
## SIUrge_resid -0.2222 0.3827
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.0000 -0.3941
## SIUrge_resid -0.3941 1.0000pdat5.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat5.2<-pdat5[pdat5.2]
coping_var=VAR(pdat5.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 1.7832, df1 = 1, df2 = 102, p-value = 0.1847summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -120.322
## Roots of the characteristic polynomial:
## 0.3661 0.1093
## Call:
## VAR(y = pdat5.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.012279 0.137945 0.089 0.929
## SIUrge_resid.l1 -0.253020 0.189477 -1.335 0.188
## const 0.005553 0.131484 0.042 0.966
##
##
## Residual standard error: 0.9662 on 51 degrees of freedom
## Multiple R-Squared: 0.03378, Adjusted R-squared: -0.004107
## F-statistic: 0.8916 on 2 and 51 DF, p-value: 0.4163
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.13562 0.08648 1.568 0.123025
## SIUrge_resid.l1 0.46309 0.11879 3.898 0.000284 ***
## const -0.01014 0.08243 -0.123 0.902575
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6057 on 51 degrees of freedom
## Multiple R-Squared: 0.2667, Adjusted R-squared: 0.2379
## F-statistic: 9.274 on 2 and 51 DF, p-value: 0.0003671
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 0.9335 0.1064
## SIUrge_resid 0.1064 0.3669
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.0000 0.1818
## SIUrge_resid 0.1818 1.0000pdat5.2<-c("Efficacy_resid", "SIUrge_resid")
pdat5.2<-pdat5[pdat5.2]
coping_var=VAR(pdat5.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 5.5153, df1 = 1, df2 = 102, p-value = 0.02078summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -111.669
## Roots of the characteristic polynomial:
## 0.4797 0.1948
## Call:
## VAR(y = pdat5.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.2004322 0.1331288 1.506 0.1384
## SIUrge_resid.l1 -0.3792600 0.1614928 -2.348 0.0228 *
## const 0.0007672 0.1084304 0.007 0.9944
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7966 on 51 degrees of freedom
## Multiple R-Squared: 0.1685, Adjusted R-squared: 0.1359
## F-statistic: 5.169 on 2 and 51 DF, p-value: 0.009038
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 -0.004140 0.103641 -0.040 0.968290
## SIUrge_resid.l1 0.474115 0.125722 3.771 0.000424 ***
## const -0.009237 0.084413 -0.109 0.913292
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6201 on 51 degrees of freedom
## Multiple R-Squared: 0.2314, Adjusted R-squared: 0.2012
## F-statistic: 7.676 on 2 and 51 DF, p-value: 0.001219
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.63456 -0.06052
## SIUrge_resid -0.06052 0.38458
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 -0.1225
## SIUrge_resid -0.1225 1.0000207
Specifying the data structure for impuation
MImodel = pdat7[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag all_coping_crisisline.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 560k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat7.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat7.1<-pdat7.imp[vars]
pdat7.2<- do.call(rbind, apply(pdat7.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA,
all_coping_crisisline.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp",
"all_coping_crisisline.imp")
pdat7.3<-pdat7.imp[vars]
pdat7.4 <- do.call(rbind, apply(pdat7.3, 1, function(x) {rbind(na.df, x)}))
pdat7.imp<-cbind(pdat7.4, pdat7.2)
pdat7.imp$Day<-c(1:56)Creating splines
pdat7.imp<-data.frame(na.spline(pdat7.imp))
pdat7.imp<-round(pdat7.imp)
pdat7.imp$SIUrge.imp[pdat7.imp$SIUrge.imp>7]<-7
pdat7.imp$SIUrge.imp[pdat7.imp$SIUrge.imp<0]<-0
pdat7.imp$Self_Efficacy.imp[pdat7.imp$Self_Efficacy.imp>10]<-10
pdat7.imp$Self_Efficacy.imp[pdat7.imp$Self_Efficacy.imp<0]<-0pdat7.imp <- pdat7.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_crisisline.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat7.imp[cols] <- lapply(pdat7.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat7, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat7.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat7.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod4<-glm(all_coping_crisisline.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_crisisline_resid<-as.numeric(rstandard(mod4))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat7.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat7.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat7.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat7.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat7<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_crisisline_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Calculating Difference Scores
attach(pdat7)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_crisisline_resid, Coping_dis_rel_resid,
## Coping_sum_3avg_resid, Coping_sum_resid, Coping_TalkFamily_resid,
## Coping_TalkFriend_resid, Coping_TalkMH_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_resid## The following objects are masked from pdat5:
##
## Coping_sum_3avg_resid, Coping_sum_resid, Coping_TalkFamily_resid,
## Coping_TalkFriend_resid, Coping_TalkMH_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_resid## The following objects are masked from pdat4:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat2:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_residCoping_TalkFamily_resid = diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_crisisline_resid = diff(Coping_crisisline_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat7<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid, Coping_crisisline_resid))
pdat7$day<-c(1:55)Person 7: Same Day models with SI Urge Predicting Changes in Coping
pdat7.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 14.922, df1 = 1, df2 = 102, p-value = 0.0001971summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -121.926
## Roots of the characteristic polynomial:
## 0.2611 0.2611
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.044624 0.129921 -0.343 0.732654
## SIUrge_resid.l1 -0.569175 0.147346 -3.863 0.000318 ***
## const -0.009662 0.134673 -0.072 0.943085
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9887 on 51 degrees of freedom
## Multiple R-Squared: 0.2264, Adjusted R-squared: 0.196
## F-statistic: 7.461 on 2 and 51 DF, p-value: 0.001438
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.13946 0.07892 1.767 0.0832 .
## SIUrge_resid.l1 0.25156 0.08950 2.811 0.0070 **
## const -0.06232 0.08181 -0.762 0.4497
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6005 on 51 degrees of freedom
## Multiple R-Squared: 0.1669, Adjusted R-squared: 0.1343
## F-statistic: 5.11 on 2 and 51 DF, p-value: 0.009488
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 0.9774 0.0327
## SIUrge_resid 0.0327 0.3607
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.00000 0.05507
## SIUrge_resid 0.05507 1.00000pdat7.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 4.4793, df1 = 1, df2 = 102, p-value = 0.03674summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -131.01
## Roots of the characteristic polynomial:
## 0.113 0.113
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.06194 0.14295 -0.433 0.6666
## SIUrge_resid.l1 -0.37574 0.17753 -2.116 0.0392 *
## const -0.02697 0.15944 -0.169 0.8663
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.171 on 51 degrees of freedom
## Multiple R-Squared: 0.08074, Adjusted R-squared: 0.04469
## F-statistic: 2.24 on 2 and 51 DF, p-value: 0.1169
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.07635 0.07479 1.021 0.31213
## SIUrge_resid.l1 0.25693 0.09288 2.766 0.00788 **
## const -0.06088 0.08342 -0.730 0.46883
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6124 on 51 degrees of freedom
## Multiple R-Squared: 0.1336, Adjusted R-squared: 0.09967
## F-statistic: 3.934 on 2 and 51 DF, p-value: 0.02578
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.3703 -0.1481
## SIUrge_resid -0.1481 0.3751
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.0000 -0.2065
## SIUrge_resid -0.2065 1.0000pdat7.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 0.076027, df1 = 1, df2 = 102, p-value = 0.7833summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -134.452
## Roots of the characteristic polynomial:
## 0.207 0.02494
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.01113 0.14426 0.077 0.939
## SIUrge_resid.l1 -0.05141 0.18645 -0.276 0.784
## const -0.03014 0.16600 -0.182 0.857
##
##
## Residual standard error: 1.218 on 51 degrees of freedom
## Multiple R-Squared: 0.00149, Adjusted R-squared: -0.03767
## F-statistic: 0.03806 on 2 and 51 DF, p-value: 0.9627
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.05263 0.07292 0.722 0.4738
## SIUrge_resid.l1 0.22084 0.09425 2.343 0.0231 *
## const -0.06237 0.08391 -0.743 0.4607
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6155 on 51 degrees of freedom
## Multiple R-Squared: 0.1249, Adjusted R-squared: 0.09056
## F-statistic: 3.639 on 2 and 51 DF, p-value: 0.03332
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.48279 0.05343
## SIUrge_resid 0.05343 0.37887
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 0.07128
## SIUrge_resid 0.07128 1.00000pdat7.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 3.7054, df1 = 1, df2 = 102, p-value = 0.05702summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -125.271
## Roots of the characteristic polynomial:
## 0.2329 0.2329
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.01279 0.13532 -0.095 0.9251
## SIUrge_resid.l1 -0.30969 0.16088 -1.925 0.0598 .
## const -0.01706 0.14751 -0.116 0.9084
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.083 on 51 degrees of freedom
## Multiple R-Squared: 0.06774, Adjusted R-squared: 0.03118
## F-statistic: 1.853 on 2 and 51 DF, p-value: 0.1672
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.18531 0.07284 2.544 0.01402 *
## SIUrge_resid.l1 0.24688 0.08659 2.851 0.00627 **
## const -0.05492 0.07940 -0.692 0.49223
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5828 on 51 degrees of freedom
## Multiple R-Squared: 0.2155, Adjusted R-squared: 0.1847
## F-statistic: 7.005 on 2 and 51 DF, p-value: 0.002051
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.17239 0.01911
## SIUrge_resid 0.01911 0.33963
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.00000 0.03028
## SIUrge_resid 0.03028 1.00000pdat7.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 4.4398, df1 = 1, df2 = 102, p-value = 0.03756summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -122.948
## Roots of the characteristic polynomial:
## 0.2203 0.05468
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.07825 0.13938 -0.561 0.577
## SIUrge_resid.l1 0.33461 0.15881 2.107 0.040 *
## const 0.00592 0.14040 0.042 0.967
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.031 on 51 degrees of freedom
## Multiple R-Squared: 0.08008, Adjusted R-squared: 0.04401
## F-statistic: 2.22 on 2 and 51 DF, p-value: 0.119
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.02104 0.08360 -0.252 0.8023
## SIUrge_resid.l1 0.24392 0.09525 2.561 0.0134 *
## const -0.05969 0.08421 -0.709 0.4817
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6183 on 51 degrees of freedom
## Multiple R-Squared: 0.117, Adjusted R-squared: 0.08241
## F-statistic: 3.38 on 2 and 51 DF, p-value: 0.04183
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.0626 0.2029
## SIUrge_resid 0.2029 0.3823
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.0000 0.3184
## SIUrge_resid 0.3184 1.0000pdat7.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 4.028, df1 = 1, df2 = 102, p-value = 0.0474summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -119.462
## Roots of the characteristic polynomial:
## 0.1703 0.1703
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.0003395 0.1348057 -0.003 0.9980
## SIUrge_resid.l1 0.2779621 0.1384971 2.007 0.0501 .
## const 0.0083263 0.1270940 0.066 0.9480
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.933 on 51 degrees of freedom
## Multiple R-Squared: 0.0732, Adjusted R-squared: 0.03685
## F-statistic: 2.014 on 2 and 51 DF, p-value: 0.1439
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.10458 0.08818 -1.186 0.2412
## SIUrge_resid.l1 0.23757 0.09060 2.622 0.0115 *
## const -0.05784 0.08314 -0.696 0.4898
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6103 on 51 degrees of freedom
## Multiple R-Squared: 0.1397, Adjusted R-squared: 0.1059
## F-statistic: 4.14 on 2 and 51 DF, p-value: 0.02158
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 0.87044 -0.05836
## SIUrge_resid -0.05836 0.37247
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.0000 -0.1025
## SIUrge_resid -0.1025 1.0000pdat7.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 1.7472, df1 = 1, df2 = 102, p-value = 0.1892summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -94.892
## Roots of the characteristic polynomial:
## 0.3543 0.3543
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.42290 0.13469 3.140 0.00281 **
## SIUrge_resid.l1 -0.11673 0.08831 -1.322 0.19213
## const -0.01775 0.08101 -0.219 0.82746
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5946 on 51 degrees of freedom
## Multiple R-Squared: 0.1892, Adjusted R-squared: 0.1574
## F-statistic: 5.95 on 2 and 51 DF, p-value: 0.004757
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.19862 0.13735 1.446 0.15427
## SIUrge_resid.l1 0.24192 0.09006 2.686 0.00973 **
## const -0.06304 0.08261 -0.763 0.44891
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6064 on 51 degrees of freedom
## Multiple R-Squared: 0.1508, Adjusted R-squared: 0.1175
## F-statistic: 4.527 on 2 and 51 DF, p-value: 0.0155
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.35353 -0.02912
## SIUrge_resid -0.02912 0.36767
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.00000 -0.08078
## SIUrge_resid -0.08078 1.00000pdat7.2<-c("Coping_crisisline_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_crisisline_resid
##
## data: VAR object coping_var
## F-Test = 0.66573, df1 = 1, df2 = 102, p-value = 0.4164summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_crisisline_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -118.337
## Roots of the characteristic polynomial:
## 0.2429 0.02563
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_crisisline_resid:
## ========================================================
## Coping_crisisline_resid = Coping_crisisline_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_crisisline_resid.l1 -0.05758 0.14895 -0.387 0.701
## SIUrge_resid.l1 -0.13194 0.16170 -0.816 0.418
## const 0.01317 0.13073 0.101 0.920
##
##
## Residual standard error: 0.9597 on 51 degrees of freedom
## Multiple R-Squared: 0.01289, Adjusted R-squared: -0.02582
## F-statistic: 0.3329 on 2 and 51 DF, p-value: 0.7184
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_crisisline_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_crisisline_resid.l1 0.07277 0.09548 0.762 0.4495
## SIUrge_resid.l1 0.27489 0.10365 2.652 0.0106 *
## const -0.05866 0.08380 -0.700 0.4871
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6152 on 51 degrees of freedom
## Multiple R-Squared: 0.1259, Adjusted R-squared: 0.09162
## F-statistic: 3.673 on 2 and 51 DF, p-value: 0.03235
##
##
##
## Covariance matrix of residuals:
## Coping_crisisline_resid SIUrge_resid
## Coping_crisisline_resid 0.921 -0.2020
## SIUrge_resid -0.202 0.3784
##
## Correlation matrix of residuals:
## Coping_crisisline_resid SIUrge_resid
## Coping_crisisline_resid 1.0000 -0.3422
## SIUrge_resid -0.3422 1.0000pdat7.2<-c("Efficacy_resid", "SIUrge_resid")
pdat7.2<-pdat7[pdat7.2]
coping_var=VAR(pdat7.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 8.2977, df1 = 1, df2 = 102, p-value = 0.004839summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -69.063
## Roots of the characteristic polynomial:
## 0.527 0.527
## Call:
## VAR(y = pdat7.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.54732 0.10874 5.033 6.37e-06 ***
## SIUrge_resid.l1 -0.21534 0.07476 -2.881 0.00579 **
## const 0.03590 0.06891 0.521 0.60468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5035 on 51 degrees of freedom
## Multiple R-Squared: 0.4017, Adjusted R-squared: 0.3782
## F-statistic: 17.12 on 2 and 51 DF, p-value: 2.051e-06
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.66248 0.09617 6.889 8.15e-09 ***
## SIUrge_resid.l1 0.24681 0.06611 3.733 0.000477 ***
## const -0.01816 0.06094 -0.298 0.766900
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.4453 on 51 degrees of freedom
## Multiple R-Squared: 0.5421, Adjusted R-squared: 0.5241
## F-statistic: 30.18 on 2 and 51 DF, p-value: 2.241e-09
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.25350 0.02546
## SIUrge_resid 0.02546 0.19826
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 0.1135
## SIUrge_resid 0.1135 1.0000212
Specifying the data structure for imputation
MImodel = pdat11[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 365k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat11.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat11.1<-pdat11.imp[vars]
pdat11.2<- do.call(rbind, apply(pdat11.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat11.3<-pdat11.imp[vars]
pdat11.4 <- do.call(rbind, apply(pdat11.3, 1, function(x) {rbind(na.df, x)}))
pdat11.imp<-cbind(pdat11.4, pdat11.2)
pdat11.imp$Day<-c(1:56)Creating splines
pdat11.imp<-data.frame(na.spline(pdat11.imp))
pdat11.imp<-round(pdat11.imp)
pdat11.imp$SIUrge.imp[pdat11.imp$SIUrge.imp>7]<-7
pdat11.imp$SIUrge.imp[pdat11.imp$SIUrge.imp<0]<-0
pdat11.imp$Self_Efficacy.imp[pdat11.imp$Self_Efficacy.imp>10]<-10
pdat11.imp$Self_Efficacy.imp[pdat11.imp$Self_Efficacy.imp<0]<-0cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat11.imp <- pdat11.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
pdat11.imp[cols] <- lapply(pdat11.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat11, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat11.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat11.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat11.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat11.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat11.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat11.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat11.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat11.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat11.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat11.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat11<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_any_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))## Warning in base::cbind(...): number of rows of result is not a multiple of
## vector length (arg 6)Person 11: Calculating the difference scores
attach(pdat11)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat11<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat11$day<-c(1:55)Person 11: Same Day models with SI Urge Predicting Changes in Coping
pdat11.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 4.1814, df1 = 1, df2 = 102, p-value = 0.04344summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -95.092
## Roots of the characteristic polynomial:
## 0.3332 0.3332
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.14134 0.13317 1.061 0.294
## SIUrge_resid.l1 -0.15311 0.07488 -2.045 0.046 *
## const -0.02750 0.06310 -0.436 0.665
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.4626 on 51 degrees of freedom
## Multiple R-Squared: 0.09846, Adjusted R-squared: 0.06311
## F-statistic: 2.785 on 2 and 51 DF, p-value: 0.07114
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.37254 0.22449 1.659 0.10316
## SIUrge_resid.l1 0.38196 0.12623 3.026 0.00388 **
## const 0.02298 0.10637 0.216 0.82985
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7799 on 51 degrees of freedom
## Multiple R-Squared: 0.1824, Adjusted R-squared: 0.1504
## F-statistic: 5.69 on 2 and 51 DF, p-value: 0.005878
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.21401 0.00803
## SIUrge_resid 0.00803 0.60819
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.00000 0.02226
## SIUrge_resid 0.02226 1.00000pdat11.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 0.23877, df1 = 1, df2 = 102, p-value = 0.6261summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -135.116
## Roots of the characteristic polynomial:
## 0.3727 0.04173
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.01128 0.14166 -0.080 0.937
## SIUrge_resid.l1 -0.07792 0.15946 -0.489 0.627
## const -0.01142 0.13244 -0.086 0.932
##
##
## Residual standard error: 0.9732 on 51 degrees of freedom
## Multiple R-Squared: 0.00466, Adjusted R-squared: -0.03437
## F-statistic: 0.1194 on 2 and 51 DF, p-value: 0.8877
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.150055 0.114635 -1.309 0.1964
## SIUrge_resid.l1 0.342208 0.129045 2.652 0.0106 *
## const 0.009392 0.107176 0.088 0.9305
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7875 on 51 degrees of freedom
## Multiple R-Squared: 0.1663, Adjusted R-squared: 0.1336
## F-statistic: 5.087 on 2 and 51 DF, p-value: 0.009675
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 0.9470 -0.1204
## SIUrge_resid -0.1204 0.6202
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.000 -0.157
## SIUrge_resid -0.157 1.000pdat11.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 2.2741, df1 = 1, df2 = 102, p-value = 0.1346summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -127.679
## Roots of the characteristic polynomial:
## 0.2522 0.2522
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.01162 0.13734 0.085 0.933
## SIUrge_resid.l1 0.21463 0.14233 1.508 0.138
## const -0.02523 0.11961 -0.211 0.834
##
##
## Residual standard error: 0.8786 on 51 degrees of freedom
## Multiple R-Squared: 0.04269, Adjusted R-squared: 0.005153
## F-statistic: 1.137 on 2 and 51 DF, p-value: 0.3287
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.277494 0.118969 -2.332 0.02366 *
## SIUrge_resid.l1 0.350161 0.123290 2.840 0.00646 **
## const 0.003956 0.103614 0.038 0.96970
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7611 on 51 degrees of freedom
## Multiple R-Squared: 0.2214, Adjusted R-squared: 0.1908
## F-statistic: 7.249 on 2 and 51 DF, p-value: 0.001695
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 0.7719 -0.1105
## SIUrge_resid -0.1105 0.5792
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.0000 -0.1653
## SIUrge_resid -0.1653 1.0000pdat11.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 0.44697, df1 = 1, df2 = 102, p-value = 0.5053summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -137.709
## Roots of the characteristic polynomial:
## 0.3516 0.02228
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.01376 0.14051 -0.098 0.922
## SIUrge_resid.l1 0.10976 0.16418 0.669 0.507
## const -0.02738 0.13723 -0.199 0.843
##
##
## Residual standard error: 1.008 on 51 degrees of freedom
## Multiple R-Squared: 0.008692, Adjusted R-squared: -0.03018
## F-statistic: 0.2236 on 2 and 51 DF, p-value: 0.8004
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.119946 0.110325 -1.087 0.28206
## SIUrge_resid.l1 0.387591 0.128912 3.007 0.00409 **
## const 0.007813 0.107754 0.073 0.94248
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7915 on 51 degrees of freedom
## Multiple R-Squared: 0.1578, Adjusted R-squared: 0.1248
## F-statistic: 4.778 on 2 and 51 DF, p-value: 0.01253
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.01621 0.07791
## SIUrge_resid 0.07791 0.62651
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.00000 0.09764
## SIUrge_resid 0.09764 1.00000pdat11.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 2.5672, df1 = 1, df2 = 102, p-value = 0.1122summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -136.335
## Roots of the characteristic polynomial:
## 0.2903 0.0672
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.03557 0.13822 -0.257 0.798
## SIUrge_resid.l1 0.25737 0.16063 1.602 0.115
## const -0.02670 0.13376 -0.200 0.843
##
##
## Residual standard error: 0.9825 on 51 degrees of freedom
## Multiple R-Squared: 0.04793, Adjusted R-squared: 0.01059
## F-statistic: 1.284 on 2 and 51 DF, p-value: 0.2858
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.130103 0.111148 -1.171 0.2472
## SIUrge_resid.l1 0.393031 0.129167 3.043 0.0037 **
## const 0.007701 0.107557 0.072 0.9432
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7901 on 51 degrees of freedom
## Multiple R-Squared: 0.1608, Adjusted R-squared: 0.1279
## F-statistic: 4.888 on 2 and 51 DF, p-value: 0.01143
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.96540 0.05803
## SIUrge_resid 0.05803 0.62426
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.00000 0.07475
## SIUrge_resid 0.07475 1.00000pdat11.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 7.6837, df1 = 1, df2 = 102, p-value = 0.006625summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -143.228
## Roots of the characteristic polynomial:
## 0.2667 0.2667
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.05086 0.13712 -0.371 0.71222
## SIUrge_resid.l1 0.51412 0.18547 2.772 0.00776 **
## const 0.03444 0.15479 0.222 0.82482
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.137 on 51 degrees of freedom
## Multiple R-Squared: 0.1309, Adjusted R-squared: 0.09685
## F-statistic: 3.842 on 2 and 51 DF, p-value: 0.02792
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.178137 0.093243 -1.910 0.06170 .
## SIUrge_resid.l1 0.402400 0.126124 3.191 0.00243 **
## const 0.009249 0.105257 0.088 0.93032
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7734 on 51 degrees of freedom
## Multiple R-Squared: 0.1958, Adjusted R-squared: 0.1643
## F-statistic: 6.21 on 2 and 51 DF, p-value: 0.003856
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.2937 -0.0171
## SIUrge_resid -0.0171 0.5982
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 -0.01944
## SIUrge_resid -0.01944 1.00000pdat11.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 4.7939, df1 = 1, df2 = 102, p-value = 0.03084summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -106.746
## Roots of the characteristic polynomial:
## 0.4221 0.4221
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.34133 0.09954 3.429 0.00121 **
## SIUrge_resid.l1 0.20573 0.09396 2.190 0.03316 *
## const -0.03330 0.07922 -0.420 0.67603
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5812 on 51 degrees of freedom
## Multiple R-Squared: 0.2408, Adjusted R-squared: 0.211
## F-statistic: 8.088 on 2 and 51 DF, p-value: 0.0008896
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 -0.26260 0.13209 -1.988 0.05219 .
## SIUrge_resid.l1 0.36375 0.12469 2.917 0.00524 **
## const 0.02281 0.10513 0.217 0.82913
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7713 on 51 degrees of freedom
## Multiple R-Squared: 0.2003, Adjusted R-squared: 0.1689
## F-statistic: 6.386 on 2 and 51 DF, p-value: 0.00335
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.33784 0.02608
## SIUrge_resid 0.02608 0.59493
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.00000 0.05817
## SIUrge_resid 0.05817 1.00000pdat11.2<-c("Efficacy_resid", "SIUrge_resid")
pdat11.2<-pdat11[pdat11.2]
coping_var=VAR(pdat11.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 5.0489, df1 = 1, df2 = 102, p-value = 0.0268summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -101.723
## Roots of the characteristic polynomial:
## 0.4845 0.4845
## Call:
## VAR(y = pdat11.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.56586 0.11096 5.099 5.06e-06 ***
## SIUrge_resid.l1 -0.20677 0.09202 -2.247 0.029 *
## const 0.03473 0.07422 0.468 0.642
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5454 on 51 degrees of freedom
## Multiple R-Squared: 0.3434, Adjusted R-squared: 0.3176
## F-statistic: 13.34 on 2 and 51 DF, p-value: 2.195e-05
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.350932 0.155299 2.260 0.0281 *
## SIUrge_resid.l1 0.286566 0.128786 2.225 0.0305 *
## const 0.009873 0.103879 0.095 0.9247
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7633 on 51 degrees of freedom
## Multiple R-Squared: 0.2167, Adjusted R-squared: 0.186
## F-statistic: 7.056 on 2 and 51 DF, p-value: 0.001972
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.29749 0.08388
## SIUrge_resid 0.08388 0.58269
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 0.2015
## SIUrge_resid 0.2015 1.0000214
Specifying data structure for imputation
MImodel = pdat13[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Person 13: Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag*
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag*
## * Please inspect the loggedEvents## Warning: Number of logged events: 652k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat13.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat13.1<-pdat13.imp[vars]
pdat13.2<- do.call(rbind, apply(pdat13.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat13.3<-pdat13.imp[vars]
pdat13.4 <- do.call(rbind, apply(pdat13.3, 1, function(x) {rbind(na.df, x)}))
pdat13.imp<-cbind(pdat13.4, pdat13.2)
pdat13.imp$Day<-c(1:56)Creating splines
pdat13.imp<-data.frame(na.spline(pdat13.imp))
pdat13.imp<-round(pdat13.imp)
pdat13.imp$SIUrge.imp[pdat13.imp$SIUrge.imp>7]<-7
pdat13.imp$SIUrge.imp[pdat13.imp$SIUrge.imp<0]<-0
pdat13.imp$Self_Efficacy.imp[pdat13.imp$Self_Efficacy.imp>10]<-10
pdat13.imp$Self_Efficacy.imp[pdat13.imp$Self_Efficacy.imp<0]<-0pdat13.imp <- pdat13.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat13.imp[cols] <- lapply(pdat13.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat13, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat13.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat13.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat13.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat13.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat13.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat13.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat13<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Person 13: Calculating Difference Scores
attach(pdat13)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid = diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat13<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat13$day<-c(1:55)Person 13: Same Day Models with SI Urge Predicting Changes in Coping
pdat13.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 0.30912, df1 = 1, df2 = 102, p-value = 0.5794summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -110.207
## Roots of the characteristic polynomial:
## 0.323 0.323
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.20153 0.14362 1.403 0.167
## SIUrge_resid.l1 -0.07443 0.13387 -0.556 0.581
## const 0.02495 0.10102 0.247 0.806
##
##
## Residual standard error: 0.7413 on 51 degrees of freedom
## Multiple R-Squared: 0.03907, Adjusted R-squared: 0.00139
## F-statistic: 1.037 on 2 and 51 DF, p-value: 0.3619
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.287698 0.127112 2.263 0.02790 *
## SIUrge_resid.l1 0.411310 0.118481 3.472 0.00106 **
## const 0.005973 0.089408 0.067 0.94699
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6561 on 51 degrees of freedom
## Multiple R-Squared: 0.2858, Adjusted R-squared: 0.2578
## F-statistic: 10.21 on 2 and 51 DF, p-value: 0.0001871
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.54948 0.09379
## SIUrge_resid 0.09379 0.43041
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.0000 0.1928
## SIUrge_resid 0.1928 1.0000pdat13.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 2.4319, df1 = 1, df2 = 102, p-value = 0.122summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -143.409
## Roots of the characteristic polynomial:
## 0.2405 0.2405
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.05755 0.14572 0.395 0.695
## SIUrge_resid.l1 0.40051 0.25682 1.559 0.125
## const 0.01090 0.19049 0.057 0.955
##
##
## Residual standard error: 1.396 on 51 degrees of freedom
## Multiple R-Squared: 0.04551, Adjusted R-squared: 0.008084
## F-statistic: 1.216 on 2 and 51 DF, p-value: 0.3049
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.084241 0.070875 -1.189 0.24011
## SIUrge_resid.l1 0.419025 0.124909 3.355 0.00151 **
## const 0.002952 0.092645 0.032 0.97471
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6789 on 51 degrees of freedom
## Multiple R-Squared: 0.2353, Adjusted R-squared: 0.2053
## F-statistic: 7.845 on 2 and 51 DF, p-value: 0.00107
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.9483 -0.3452
## SIUrge_resid -0.3452 0.4609
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.0000 -0.3643
## SIUrge_resid -0.3643 1.0000pdat13.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 0.57991, df1 = 1, df2 = 102, p-value = 0.4481summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -138.324
## Roots of the characteristic polynomial:
## 0.4479 0.0275
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.01893 0.14183 -0.133 0.894
## SIUrge_resid.l1 -0.16842 0.22116 -0.762 0.450
## const 0.03965 0.16647 0.238 0.813
##
##
## Residual standard error: 1.22 on 51 degrees of freedom
## Multiple R-Squared: 0.01124, Adjusted R-squared: -0.02753
## F-statistic: 0.29 on 2 and 51 DF, p-value: 0.7495
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.12869 0.07793 1.651 0.104842
## SIUrge_resid.l1 0.49437 0.12153 4.068 0.000165 ***
## const 0.01612 0.09147 0.176 0.860809
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6705 on 51 degrees of freedom
## Multiple R-Squared: 0.254, Adjusted R-squared: 0.2247
## F-statistic: 8.681 on 2 and 51 DF, p-value: 0.0005692
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.4890 -0.1561
## SIUrge_resid -0.1561 0.4496
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.0000 -0.1908
## SIUrge_resid -0.1908 1.0000pdat13.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 6.4443, df1 = 1, df2 = 102, p-value = 0.01264summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -127.851
## Roots of the characteristic polynomial:
## 0.4469 0.08466
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.10105 0.14541 -0.695 0.4903
## SIUrge_resid.l1 -0.45370 0.17872 -2.539 0.0142 *
## const 0.03468 0.13160 0.264 0.7932
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9657 on 51 degrees of freedom
## Multiple R-Squared: 0.1122, Adjusted R-squared: 0.07737
## F-statistic: 3.222 on 2 and 51 DF, p-value: 0.04811
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.019783 0.103590 0.191 0.849301
## SIUrge_resid.l1 0.463260 0.127320 3.639 0.000639 ***
## const 0.009068 0.093750 0.097 0.923326
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.688 on 51 degrees of freedom
## Multiple R-Squared: 0.2146, Adjusted R-squared: 0.1839
## F-statistic: 6.97 on 2 and 51 DF, p-value: 0.002109
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 0.93262 -0.06097
## SIUrge_resid -0.06097 0.47331
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 -0.09176
## SIUrge_resid -0.09176 1.00000pdat13.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 3.9739, df1 = 1, df2 = 102, p-value = 0.04888summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -131.933
## Roots of the characteristic polynomial:
## 0.3774 0.06035
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.06600 0.13868 -0.476 0.6362
## SIUrge_resid.l1 -0.39130 0.19629 -1.993 0.0516 .
## const 0.02429 0.14619 0.166 0.8687
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.073 on 51 degrees of freedom
## Multiple R-Squared: 0.07229, Adjusted R-squared: 0.03591
## F-statistic: 1.987 on 2 and 51 DF, p-value: 0.1476
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.143171 0.086699 1.651 0.104811
## SIUrge_resid.l1 0.503748 0.122721 4.105 0.000146 ***
## const 0.005458 0.091394 0.060 0.952611
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6705 on 51 degrees of freedom
## Multiple R-Squared: 0.254, Adjusted R-squared: 0.2247
## F-statistic: 8.681 on 2 and 51 DF, p-value: 0.0005691
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.15028 -0.08964
## SIUrge_resid -0.08964 0.44961
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.0000 -0.1247
## SIUrge_resid -0.1247 1.0000pdat13.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 3.7242, df1 = 1, df2 = 102, p-value = 0.05641summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -127.307
## Roots of the characteristic polynomial:
## 0.2313 0.2313
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.01485 0.12775 -0.116 0.9079
## SIUrge_resid.l1 -0.34115 0.17678 -1.930 0.0592 .
## const 0.01464 0.13512 0.108 0.9141
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9914 on 51 degrees of freedom
## Multiple R-Squared: 0.06805, Adjusted R-squared: 0.03151
## F-statistic: 1.862 on 2 and 51 DF, p-value: 0.1658
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.17731 0.08514 2.083 0.042321 *
## SIUrge_resid.l1 0.47128 0.11782 4.000 0.000205 ***
## const 0.01288 0.09005 0.143 0.886833
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6607 on 51 degrees of freedom
## Multiple R-Squared: 0.2757, Adjusted R-squared: 0.2473
## F-statistic: 9.706 on 2 and 51 DF, p-value: 0.000268
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.982794 -0.006616
## SIUrge_resid -0.006616 0.436524
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.0000 -0.0101
## SIUrge_resid -0.0101 1.0000pdat13.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 11.026, df1 = 1, df2 = 102, p-value = 0.001247summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -130.994
## Roots of the characteristic polynomial:
## 0.4276 0.0633
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.10411 0.13067 -0.797 0.42930
## SIUrge_resid.l1 0.62177 0.18725 3.321 0.00167 **
## const -0.03348 0.13939 -0.240 0.81116
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.022 on 51 degrees of freedom
## Multiple R-Squared: 0.1778, Adjusted R-squared: 0.1455
## F-statistic: 5.513 on 2 and 51 DF, p-value: 0.006798
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.034896 0.087840 -0.397 0.692825
## SIUrge_resid.l1 0.468416 0.125875 3.721 0.000495 ***
## const 0.007566 0.093700 0.081 0.935958
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6872 on 51 degrees of freedom
## Multiple R-Squared: 0.2165, Adjusted R-squared: 0.1858
## F-statistic: 7.047 on 2 and 51 DF, p-value: 0.001985
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.04490 0.04072
## SIUrge_resid 0.04072 0.47219
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 0.05797
## SIUrge_resid 0.05797 1.00000pdat13.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 0.58239, df1 = 1, df2 = 102, p-value = 0.4471summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -119.966
## Roots of the characteristic polynomial:
## 0.3305 0.2965
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.18041 0.12942 1.394 0.169
## SIUrge_resid.l1 -0.11540 0.15122 -0.763 0.449
## const 0.04498 0.11561 0.389 0.699
##
##
## Residual standard error: 0.8482 on 51 degrees of freedom
## Multiple R-Squared: 0.04518, Adjusted R-squared: 0.007737
## F-statistic: 1.207 on 2 and 51 DF, p-value: 0.3076
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.15106 0.10286 1.469 0.148088
## SIUrge_resid.l1 0.44665 0.12018 3.716 0.000503 ***
## const 0.01206 0.09188 0.131 0.896051
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6741 on 51 degrees of freedom
## Multiple R-Squared: 0.246, Adjusted R-squared: 0.2164
## F-statistic: 8.318 on 2 and 51 DF, p-value: 0.0007471
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.71942 0.00856
## SIUrge_resid 0.00856 0.45443
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.00000 0.01497
## SIUrge_resid 0.01497 1.00000pdat13.2<-c("Efficacy_resid", "SIUrge_resid")
pdat13.2<-pdat13[pdat13.2]
coping_var=VAR(pdat13.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 44.283, df1 = 1, df2 = 102, p-value = 1.447e-09summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -86.59
## Roots of the characteristic polynomial:
## 0.6438 0.6438
## Call:
## VAR(y = pdat13.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.26470 0.09113 2.905 0.00542 **
## SIUrge_resid.l1 -0.62554 0.09400 -6.655 1.91e-08 ***
## const -0.01980 0.07017 -0.282 0.77893
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5142 on 51 degrees of freedom
## Multiple R-Squared: 0.5599, Adjusted R-squared: 0.5427
## F-statistic: 32.45 on 2 and 51 DF, p-value: 8.118e-10
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.426888 0.106312 4.015 0.000195 ***
## SIUrge_resid.l1 0.556916 0.109665 5.078 5.44e-06 ***
## const -0.008608 0.081862 -0.105 0.916668
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5999 on 51 degrees of freedom
## Multiple R-Squared: 0.4029, Adjusted R-squared: 0.3795
## F-statistic: 17.2 on 2 and 51 DF, p-value: 1.949e-06
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.26441 0.01429
## SIUrge_resid 0.01429 0.35987
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.00000 0.04632
## SIUrge_resid 0.04632 1.00000Person 222
Specifying the data structure for imputation
MImodel = pdat20[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Person 20: Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* SIUrge.lag* Self_Efficacy.lag*
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 539k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat20.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat20.1<-pdat20.imp[vars]
pdat20.2<- do.call(rbind, apply(pdat20.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat20.3<-pdat20.imp[vars]
pdat20.4 <- do.call(rbind, apply(pdat20.3, 1, function(x) {rbind(na.df, x)}))
pdat20.imp<-cbind(pdat20.4, pdat20.2)
pdat20.imp$Day<-c(1:56)Creating splines
pdat20.imp<-data.frame(na.spline(pdat20.imp))
pdat20.imp<-round(pdat20.imp)
pdat20.imp$SIUrge.imp[pdat20.imp$SIUrge.imp>7]<-7
pdat20.imp$SIUrge.imp[pdat20.imp$SIUrge.imp<0]<-0
pdat20.imp$Self_Efficacy.imp[pdat20.imp$Self_Efficacy.imp>10]<-10
pdat20.imp$Self_Efficacy.imp[pdat20.imp$Self_Efficacy.imp<0]<-0pdat20.imp <- pdat20.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat20.imp[cols] <- lapply(pdat20.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat20, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat20.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting standardized residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat20.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat20.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat20.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat20.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat20.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat20<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))attach(pdat20)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat13:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat20<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat20$day<-c(1:55)df <- pdat20.imp %>%
dplyr::select(Day, coping_sum.imp, SIUrge.imp) %>%
tidyr::gather(key = "variable", value = "value", -Day)
a<-ggplot(df, aes(x = Day, y = value)) +
geom_line(aes(linetype = variable), size = 1) + labs(y="Value", x = "Day of Study") + theme_bw()
a<-a+scale_linetype_manual(values=c("solid", "dashed"), name="Variable", labels=c("Suicidal Urge", "Sum of Coping Strategies"))
jpeg("Person 20.SUM.jpeg", res=300, height=6, width=9, units="in")
a
dev.off()## quartz_off_screen
## 2Person 20: Same Day Models with SI Urge Predicting Coping
pdat20.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 0.16624, df1 = 1, df2 = 102, p-value = 0.6843summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -89.977
## Roots of the characteristic polynomial:
## 0.3626 0.0849
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 -0.093951 0.138034 -0.681 0.499
## SIUrge_resid.l1 -0.029396 0.072097 -0.408 0.685
## const -0.009174 0.058170 -0.158 0.875
##
##
## Residual standard error: 0.4267 on 51 degrees of freedom
## Multiple R-Squared: 0.01168, Adjusted R-squared: -0.02708
## F-statistic: 0.3013 on 2 and 51 DF, p-value: 0.7412
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.14050 0.24885 0.565 0.57481
## SIUrge_resid.l1 0.37164 0.12997 2.859 0.00614 **
## const 0.01101 0.10487 0.105 0.91677
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7692 on 51 degrees of freedom
## Multiple R-Squared: 0.1407, Adjusted R-squared: 0.107
## F-statistic: 4.175 on 2 and 51 DF, p-value: 0.02092
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.182060 -0.009222
## SIUrge_resid -0.009222 0.591702
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.0000 -0.0281
## SIUrge_resid -0.0281 1.0000pdat20.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 6.9682, df1 = 1, df2 = 102, p-value = 0.0096summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -120.136
## Roots of the characteristic polynomial:
## 0.2094 0.1337
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.035342 0.131868 -0.268 0.790
## SIUrge_resid.l1 -0.335525 0.127105 -2.640 0.011 *
## const -0.009713 0.102154 -0.095 0.925
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7502 on 51 degrees of freedom
## Multiple R-Squared: 0.1202, Adjusted R-squared: 0.08572
## F-statistic: 3.485 on 2 and 51 DF, p-value: 0.03815
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.12331 0.13452 0.917 0.36364
## SIUrge_resid.l1 0.37846 0.12966 2.919 0.00522 **
## const 0.01604 0.10421 0.154 0.87826
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7653 on 51 degrees of freedom
## Multiple R-Squared: 0.1493, Adjusted R-squared: 0.116
## F-statistic: 4.477 on 2 and 51 DF, p-value: 0.01617
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 0.56286 0.02791
## SIUrge_resid 0.02791 0.58575
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.0000 0.0486
## SIUrge_resid 0.0486 1.0000pdat20.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 0.58351, df1 = 1, df2 = 102, p-value = 0.4467summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -143.503
## Roots of the characteristic polynomial:
## 0.3621 0.0003779
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.022813 0.142420 -0.160 0.873
## SIUrge_resid.l1 -0.154251 0.201931 -0.764 0.448
## const -0.002242 0.159262 -0.014 0.989
##
##
## Residual standard error: 1.17 on 51 degrees of freedom
## Multiple R-Squared: 0.01131, Adjusted R-squared: -0.02746
## F-statistic: 0.2918 on 2 and 51 DF, p-value: 0.7482
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.05599 0.09361 0.598 0.55240
## SIUrge_resid.l1 0.38458 0.13272 2.898 0.00553 **
## const 0.01411 0.10468 0.135 0.89328
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7689 on 51 degrees of freedom
## Multiple R-Squared: 0.1414, Adjusted R-squared: 0.1077
## F-statistic: 4.198 on 2 and 51 DF, p-value: 0.02052
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.3686 -0.1663
## SIUrge_resid -0.1663 0.5913
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.0000 -0.1849
## SIUrge_resid -0.1849 1.0000pdat20.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 1.0193, df1 = 1, df2 = 102, p-value = 0.3151summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -130.633
## Roots of the characteristic polynomial:
## 0.3351 0.02709
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.01218 0.13896 -0.088 0.930
## SIUrge_resid.l1 -0.15500 0.15353 -1.010 0.317
## const -0.02948 0.12366 -0.238 0.813
##
##
## Residual standard error: 0.9078 on 51 degrees of freedom
## Multiple R-Squared: 0.0196, Adjusted R-squared: -0.01885
## F-statistic: 0.5098 on 2 and 51 DF, p-value: 0.6036
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.08800 0.11747 0.749 0.45723
## SIUrge_resid.l1 0.37437 0.12979 2.884 0.00573 **
## const 0.01691 0.10454 0.162 0.87213
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7674 on 51 degrees of freedom
## Multiple R-Squared: 0.1447, Adjusted R-squared: 0.1112
## F-statistic: 4.316 on 2 and 51 DF, p-value: 0.01855
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 0.82408 -0.01086
## SIUrge_resid -0.01086 0.58892
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 -0.01559
## SIUrge_resid -0.01559 1.00000pdat20.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 2.6012, df1 = 1, df2 = 102, p-value = 0.1099summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -138.628
## Roots of the characteristic polynomial:
## 0.2457 0.2457
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.01092 0.13681 0.080 0.937
## SIUrge_resid.l1 -0.30042 0.18627 -1.613 0.113
## const -0.01478 0.15007 -0.098 0.922
##
##
## Residual standard error: 1.102 on 51 degrees of freedom
## Multiple R-Squared: 0.04853, Adjusted R-squared: 0.01122
## F-statistic: 1.301 on 2 and 51 DF, p-value: 0.2812
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.18814 0.09209 2.043 0.04625 *
## SIUrge_resid.l1 0.35330 0.12539 2.818 0.00687 **
## const 0.01863 0.10102 0.184 0.85445
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7419 on 51 degrees of freedom
## Multiple R-Squared: 0.2007, Adjusted R-squared: 0.1694
## F-statistic: 6.404 on 2 and 51 DF, p-value: 0.003301
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.2145 0.1266
## SIUrge_resid 0.1266 0.5504
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.0000 0.1549
## SIUrge_resid 0.1549 1.0000pdat20.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 2.5726, df1 = 1, df2 = 102, p-value = 0.1118summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -124.346
## Roots of the characteristic polynomial:
## 0.2195 0.2195
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.0002533 0.1366249 -0.002 0.999
## SIUrge_resid.l1 -0.2248436 0.1401836 -1.604 0.115
## const 0.0345285 0.1131646 0.305 0.762
##
##
## Residual standard error: 0.8307 on 51 degrees of freedom
## Multiple R-Squared: 0.04802, Adjusted R-squared: 0.01069
## F-statistic: 1.286 on 2 and 51 DF, p-value: 0.2851
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.21474 0.12329 1.742 0.08757 .
## SIUrge_resid.l1 0.36745 0.12650 2.905 0.00542 **
## const 0.00783 0.10212 0.077 0.93919
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7496 on 51 degrees of freedom
## Multiple R-Squared: 0.1839, Adjusted R-squared: 0.1519
## F-statistic: 5.745 on 2 and 51 DF, p-value: 0.00562
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 0.69012 0.05837
## SIUrge_resid 0.05837 0.56197
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.00000 0.09373
## SIUrge_resid 0.09373 1.00000pdat20.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 0.1695, df1 = 1, df2 = 102, p-value = 0.6814summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -142.634
## Roots of the characteristic polynomial:
## 0.3674 0.001121
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.001593 0.139797 -0.011 0.991
## SIUrge_resid.l1 -0.078348 0.190303 -0.412 0.682
## const -0.020191 0.153558 -0.131 0.896
##
##
## Residual standard error: 1.128 on 51 degrees of freedom
## Multiple R-Squared: 0.003315, Adjusted R-squared: -0.03577
## F-statistic: 0.08482 on 2 and 51 DF, p-value: 0.9188
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.002222 0.095651 0.023 0.98155
## SIUrge_resid.l1 0.367871 0.130208 2.825 0.00673 **
## const 0.014230 0.105066 0.135 0.89280
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7716 on 51 degrees of freedom
## Multiple R-Squared: 0.1353, Adjusted R-squared: 0.1014
## F-statistic: 3.991 on 2 and 51 DF, p-value: 0.02452
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.27181 0.02153
## SIUrge_resid 0.02153 0.59539
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 0.02474
## SIUrge_resid 0.02474 1.00000pdat20.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 8.2497, df1 = 1, df2 = 102, p-value = 0.004958summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -110.853
## Roots of the characteristic polynomial:
## 0.4802 0.4802
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.41333 0.12368 3.342 0.00156 **
## SIUrge_resid.l1 -0.31394 0.10930 -2.872 0.00592 **
## const 0.02347 0.08815 0.266 0.79108
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6475 on 51 degrees of freedom
## Multiple R-Squared: 0.2704, Adjusted R-squared: 0.2418
## F-statistic: 9.45 on 2 and 51 DF, p-value: 0.0003227
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.25866 0.14287 1.810 0.07611 .
## SIUrge_resid.l1 0.36153 0.12626 2.863 0.00607 **
## const 0.01343 0.10182 0.132 0.89560
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.748 on 51 degrees of freedom
## Multiple R-Squared: 0.1876, Adjusted R-squared: 0.1557
## F-statistic: 5.887 on 2 and 51 DF, p-value: 0.00501
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.41923 0.03636
## SIUrge_resid 0.03636 0.55944
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.00000 0.07507
## SIUrge_resid 0.07507 1.00000pdat20.2<-c("Efficacy_resid", "SIUrge_resid")
pdat20.2<-pdat20[pdat20.2]
coping_var=VAR(pdat20.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 0.51947, df1 = 1, df2 = 102, p-value = 0.4727summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -125.691
## Roots of the characteristic polynomial:
## 0.3674 0.22
## Call:
## VAR(y = pdat20.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.219380 0.122465 1.791 0.0792 .
## SIUrge_resid.l1 0.101333 0.140595 0.721 0.4744
## const 0.003779 0.112926 0.033 0.9734
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8274 on 51 degrees of freedom
## Multiple R-Squared: 0.0742, Adjusted R-squared: 0.03789
## F-statistic: 2.044 on 2 and 51 DF, p-value: 0.14
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 -0.0008334 0.1142064 -0.007 0.99421
## SIUrge_resid.l1 0.3679882 0.1311132 2.807 0.00707 **
## const 0.0141261 0.1053101 0.134 0.89382
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7716 on 51 degrees of freedom
## Multiple R-Squared: 0.1353, Adjusted R-squared: 0.1014
## F-statistic: 3.991 on 2 and 51 DF, p-value: 0.02453
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.68463 0.05985
## SIUrge_resid 0.05985 0.59540
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.00000 0.09375
## SIUrge_resid 0.09375 1.00000Person 223
Specifying the data structure for imputation
MImodel = pdat21[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 251k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(as.factor(data.impute[,10]))
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat21.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat21.1<-pdat21.imp[vars]
pdat21.2<- do.call(rbind, apply(pdat21.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat21.3<-pdat21.imp[vars]
pdat21.4 <- do.call(rbind, apply(pdat21.3, 1, function(x) {rbind(na.df, x)}))
pdat21.imp<-cbind(pdat21.4, pdat21.2)
pdat21.imp$Day<-c(1:56)Creating splines
pdat21.imp<-data.frame(na.spline(pdat21.imp))
pdat21.imp<-round(pdat21.imp)
pdat21.imp$SIUrge.imp[pdat21.imp$SIUrge.imp>7]<-7
pdat21.imp$SIUrge.imp[pdat21.imp$SIUrge.imp<0]<-0
pdat21.imp$Self_Efficacy.imp[pdat21.imp$Self_Efficacy.imp>10]<-10
pdat21.imp$Self_Efficacy.imp[pdat21.imp$Self_Efficacy.imp<0]<-0pdat21.imp <- pdat21.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat21.imp[cols] <- lapply(pdat21.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat21, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat21.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting standardized residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat21.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat21.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat21.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat21.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat21.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat21<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid,Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Person 21: Calculating Difference Scores
attach(pdat21)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat20:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat13:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat21<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid,Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat21$day<-c(1:55)Person 21: Same Day Models with SI Urge Predicting Coping
pdat21.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 3.2147, df1 = 1, df2 = 102, p-value = 0.07594summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -117.684
## Roots of the characteristic polynomial:
## 0.1254 0.1254
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 -0.10358 0.13509 -0.767 0.4468
## SIUrge_resid.l1 -0.15487 0.08638 -1.793 0.0789 .
## const 0.01967 0.08093 0.243 0.8090
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5945 on 51 degrees of freedom
## Multiple R-Squared: 0.06932, Adjusted R-squared: 0.03282
## F-statistic: 1.899 on 2 and 51 DF, p-value: 0.1601
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.255330 0.210121 1.215 0.230
## SIUrge_resid.l1 0.229974 0.134352 1.712 0.093 .
## const 0.001146 0.125883 0.009 0.993
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9247 on 51 degrees of freedom
## Multiple R-Squared: 0.07943, Adjusted R-squared: 0.04333
## F-statistic: 2.2 on 2 and 51 DF, p-value: 0.1212
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.35339 0.04218
## SIUrge_resid 0.04218 0.85498
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.00000 0.07674
## SIUrge_resid 0.07674 1.00000pdat21.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 0.70497, df1 = 1, df2 = 102, p-value = 0.4031summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -156.772
## Roots of the characteristic polynomial:
## 0.2127 0.004878
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.01944 0.14073 -0.138 0.891
## SIUrge_resid.l1 -0.15023 0.17892 -0.840 0.405
## const -0.02258 0.16563 -0.136 0.892
##
##
## Residual standard error: 1.217 on 51 degrees of freedom
## Multiple R-Squared: 0.01364, Adjusted R-squared: -0.02504
## F-statistic: 0.3525 on 2 and 51 DF, p-value: 0.7046
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.037590 0.108347 0.347 0.7301
## SIUrge_resid.l1 0.237056 0.137749 1.721 0.0913 .
## const 0.006261 0.127513 0.049 0.9610
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9368 on 51 degrees of freedom
## Multiple R-Squared: 0.05501, Adjusted R-squared: 0.01795
## F-statistic: 1.484 on 2 and 51 DF, p-value: 0.2363
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.4808 -0.1486
## SIUrge_resid -0.1486 0.8777
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.0000 -0.1304
## SIUrge_resid -0.1304 1.0000pdat21.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 5.4866, df1 = 1, df2 = 102, p-value = 0.0211summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -147.2
## Roots of the characteristic polynomial:
## 0.247 0.247
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.10015 0.13953 -0.718 0.4762
## SIUrge_resid.l1 -0.38561 0.16462 -2.342 0.0231 *
## const -0.02796 0.14707 -0.190 0.8500
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.08 on 51 degrees of freedom
## Multiple R-Squared: 0.09713, Adjusted R-squared: 0.06173
## F-statistic: 2.743 on 2 and 51 DF, p-value: 0.07386
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.2400 0.1164 2.062 0.0443 *
## SIUrge_resid.l1 0.3150 0.1373 2.294 0.0259 *
## const 0.0115 0.1227 0.094 0.9257
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9011 on 51 degrees of freedom
## Multiple R-Squared: 0.1257, Adjusted R-squared: 0.09141
## F-statistic: 3.666 on 2 and 51 DF, p-value: 0.03254
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.1672 -0.2271
## SIUrge_resid -0.2271 0.8120
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.0000 -0.2333
## SIUrge_resid -0.2333 1.0000pdat21.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 0.43254, df1 = 1, df2 = 102, p-value = 0.5122summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -162.385
## Roots of the characteristic polynomial:
## 0.1772 0.05397
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.006218 0.144565 -0.043 0.966
## SIUrge_resid.l1 0.129084 0.196272 0.658 0.514
## const 0.012763 0.183490 0.070 0.945
##
##
## Residual standard error: 1.348 on 51 degrees of freedom
## Multiple R-Squared: 0.00841, Adjusted R-squared: -0.03048
## F-statistic: 0.2163 on 2 and 51 DF, p-value: 0.8063
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.085504 0.099882 -0.856 0.3960
## SIUrge_resid.l1 0.237356 0.135607 1.750 0.0861 .
## const 0.002681 0.126775 0.021 0.9832
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9313 on 51 degrees of freedom
## Multiple R-Squared: 0.0662, Adjusted R-squared: 0.02958
## F-statistic: 1.808 on 2 and 51 DF, p-value: 0.1744
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.81682 0.05444
## SIUrge_resid 0.05444 0.86728
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 0.04337
## SIUrge_resid 0.04337 1.00000pdat21.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 3.2225, df1 = 1, df2 = 102, p-value = 0.07559summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -156.166
## Roots of the characteristic polynomial:
## 0.1788 0.1788
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.06504 0.14581 -0.446 0.6574
## SIUrge_resid.l1 0.33274 0.18536 1.795 0.0786 .
## const 0.01582 0.16820 0.094 0.9255
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.236 on 51 degrees of freedom
## Multiple R-Squared: 0.05943, Adjusted R-squared: 0.02255
## F-statistic: 1.611 on 2 and 51 DF, p-value: 0.2096
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.15030 0.10866 -1.383 0.1726
## SIUrge_resid.l1 0.27724 0.13813 2.007 0.0501 .
## const 0.00118 0.12535 0.009 0.9925
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9208 on 51 degrees of freedom
## Multiple R-Squared: 0.08703, Adjusted R-squared: 0.05122
## F-statistic: 2.431 on 2 and 51 DF, p-value: 0.0981
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.5268 0.2131
## SIUrge_resid 0.2131 0.8479
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.0000 0.1873
## SIUrge_resid 0.1873 1.0000pdat21.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 2.3289, df1 = 1, df2 = 102, p-value = 0.1301summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -164.094
## Roots of the characteristic polynomial:
## 0.1804 0.1804
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.004530 0.141176 0.032 0.975
## SIUrge_resid.l1 -0.310402 0.203398 -1.526 0.133
## const 0.002394 0.190569 0.013 0.990
##
##
## Residual standard error: 1.4 on 51 degrees of freedom
## Multiple R-Squared: 0.04367, Adjusted R-squared: 0.006168
## F-statistic: 1.164 on 2 and 51 DF, p-value: 0.3202
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.10155 0.09354 1.086 0.2828
## SIUrge_resid.l1 0.22666 0.13476 1.682 0.0987 .
## const 0.01008 0.12626 0.080 0.9367
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9273 on 51 degrees of freedom
## Multiple R-Squared: 0.07417, Adjusted R-squared: 0.03787
## F-statistic: 2.043 on 2 and 51 DF, p-value: 0.1401
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.95872 0.09334
## SIUrge_resid 0.09334 0.85987
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.00000 0.07192
## SIUrge_resid 0.07192 1.00000pdat21.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 2.3892, df1 = 1, df2 = 102, p-value = 0.1253summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -157.929
## Roots of the characteristic polynomial:
## 0.2065 0.0006176
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.027302 0.143558 -0.190 0.850
## SIUrge_resid.l1 -0.279481 0.180811 -1.546 0.128
## const -0.005163 0.168152 -0.031 0.976
##
##
## Residual standard error: 1.235 on 51 degrees of freedom
## Multiple R-Squared: 0.04475, Adjusted R-squared: 0.00729
## F-statistic: 1.195 on 2 and 51 DF, p-value: 0.3112
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.02232 0.10899 0.205 0.8385
## SIUrge_resid.l1 0.23319 0.13727 1.699 0.0955 .
## const 0.00457 0.12766 0.036 0.9716
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9376 on 51 degrees of freedom
## Multiple R-Squared: 0.05356, Adjusted R-squared: 0.01644
## F-statistic: 1.443 on 2 and 51 DF, p-value: 0.2457
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.5251 -0.0843
## SIUrge_resid -0.0843 0.8790
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 -0.07281
## SIUrge_resid -0.07281 1.00000pdat21.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 0.49748, df1 = 1, df2 = 102, p-value = 0.4822summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -136.865
## Roots of the characteristic polynomial:
## 0.2784 0.2496
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.29638 0.13574 2.184 0.0336 *
## SIUrge_resid.l1 -0.08884 0.12596 -0.705 0.4838
## const 0.02305 0.11564 0.199 0.8428
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8484 on 51 degrees of freedom
## Multiple R-Squared: 0.1077, Adjusted R-squared: 0.07274
## F-statistic: 3.079 on 2 and 51 DF, p-value: 0.05465
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.009495 0.150061 0.063 0.950
## SIUrge_resid.l1 0.231543 0.139248 1.663 0.102
## const 0.005905 0.127848 0.046 0.963
##
##
## Residual standard error: 0.9379 on 51 degrees of freedom
## Multiple R-Squared: 0.05285, Adjusted R-squared: 0.01571
## F-statistic: 1.423 on 2 and 51 DF, p-value: 0.2504
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.7198 -0.1482
## SIUrge_resid -0.1482 0.8797
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.0000 -0.1862
## SIUrge_resid -0.1862 1.0000pdat21.2<-c("Efficacy_resid", "SIUrge_resid")
pdat21.2<-pdat21[pdat21.2]
coping_var=VAR(pdat21.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 62.337, df1 = 1, df2 = 102, p-value = 3.44e-12summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -109.343
## Roots of the characteristic polynomial:
## 0.6877 0.6877
## Call:
## VAR(y = pdat21.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.126074 0.090913 1.387 0.172
## SIUrge_resid.l1 -0.775457 0.098217 -7.895 2.12e-10 ***
## const -0.004827 0.088822 -0.054 0.957
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6525 on 51 degrees of freedom
## Multiple R-Squared: 0.5955, Adjusted R-squared: 0.5797
## F-statistic: 37.55 on 2 and 51 DF, p-value: 9.45e-11
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.54748 0.10583 5.173 3.9e-06 ***
## SIUrge_resid.l1 0.38412 0.11433 3.360 0.00148 **
## const 0.01737 0.10340 0.168 0.86722
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7596 on 51 degrees of freedom
## Multiple R-Squared: 0.3788, Adjusted R-squared: 0.3544
## F-statistic: 15.55 on 2 and 51 DF, p-value: 5.345e-06
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.4258 -0.1585
## SIUrge_resid -0.1585 0.5770
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 -0.3198
## SIUrge_resid -0.3198 1.0000Person 225
Specifying the data structure for imputation
MImodel = pdat23[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## * Please inspect the loggedEvents## Warning: Number of logged events: 447k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat23.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat23.1<-pdat23.imp[vars]
pdat23.2<- do.call(rbind, apply(pdat23.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat23.3<-pdat23.imp[vars]
pdat23.4 <- do.call(rbind, apply(pdat23.3, 1, function(x) {rbind(na.df, x)}))
pdat23.imp<-cbind(pdat23.4, pdat23.2)
pdat23.imp$Day<-c(1:56)Creating splines
pdat23.imp<-data.frame(na.spline(pdat23.imp))
pdat23.imp<-round(pdat23.imp)
pdat23.imp$SIUrge.imp[pdat23.imp$SIUrge.imp>7]<-7
pdat23.imp$SIUrge.imp[pdat23.imp$SIUrge.imp<0]<-0
pdat23.imp$Self_Efficacy.imp[pdat23.imp$Self_Efficacy.imp>10]<-10
pdat23.imp$Self_Efficacy.imp[pdat23.imp$Self_Efficacy.imp<0]<-0pdat23.imp <- pdat23.imp %>%
mutate_at(c(cols),list(~recode(., `4`= 0,`-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat23.imp[cols] <- lapply(pdat23.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat23, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat23.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
#Extracting standardized residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat23.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat23.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat23.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat23.imp, family=binomial(link="logit"))## Warning: glm.fit: algorithm did not converge## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurredCoping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat23.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat23.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat23.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat23.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat23.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat23.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat23<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Person 23: Calculating Difference Scores
attach(pdat23)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat21:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat20:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat13:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat23<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat23$day<-c(1:55)Person 23: Same Day Models with SI Urge Predicting Coping
pdat23.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 1.457, df1 = 1, df2 = 102, p-value = 0.2302summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -100.744
## Roots of the characteristic polynomial:
## 0.3576 0.06291
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 -0.14998 0.13851 -1.083 0.284
## SIUrge_resid.l1 -0.21413 0.17740 -1.207 0.233
## const -0.06136 0.10733 -0.572 0.570
##
##
## Residual standard error: 0.7868 on 51 degrees of freedom
## Multiple R-Squared: 0.043, Adjusted R-squared: 0.005466
## F-statistic: 1.146 on 2 and 51 DF, p-value: 0.3261
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.20638 0.08967 2.302 0.025477 *
## SIUrge_resid.l1 0.44463 0.11484 3.872 0.000309 ***
## const -0.01718 0.06948 -0.247 0.805749
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5094 on 51 degrees of freedom
## Multiple R-Squared: 0.2613, Adjusted R-squared: 0.2323
## F-statistic: 9.018 on 2 and 51 DF, p-value: 0.0004432
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.61908 0.01521
## SIUrge_resid 0.01521 0.25944
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.00000 0.03796
## SIUrge_resid 0.03796 1.00000pdat23.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 0.7529, df1 = 1, df2 = 102, p-value = 0.3876summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -124.665
## Roots of the characteristic polynomial:
## 0.3113 0.08859
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.01577 0.14582 0.108 0.914
## SIUrge_resid.l1 -0.23651 0.27257 -0.868 0.390
## const -0.05015 0.16507 -0.304 0.763
##
##
## Residual standard error: 1.213 on 51 degrees of freedom
## Multiple R-Squared: 0.01455, Adjusted R-squared: -0.0241
## F-statistic: 0.3764 on 2 and 51 DF, p-value: 0.6882
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.09100 0.06306 1.443 0.15511
## SIUrge_resid.l1 0.38414 0.11787 3.259 0.00199 **
## const -0.02780 0.07138 -0.390 0.69852
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5246 on 51 degrees of freedom
## Multiple R-Squared: 0.2165, Adjusted R-squared: 0.1858
## F-statistic: 7.047 on 2 and 51 DF, p-value: 0.001985
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.471 0.1260
## SIUrge_resid 0.126 0.2752
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.000 0.198
## SIUrge_resid 0.198 1.000pdat23.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 0.2466, df1 = 1, df2 = 102, p-value = 0.6205summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -121.884
## Roots of the characteristic polynomial:
## 0.3947 0.009547
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.0005145 0.1397611 0.004 0.997
## SIUrge_resid.l1 -0.1231293 0.2479514 -0.497 0.622
## const -0.0355676 0.1513426 -0.235 0.815
##
##
## Residual standard error: 1.112 on 51 degrees of freedom
## Multiple R-Squared: 0.004815, Adjusted R-squared: -0.03421
## F-statistic: 0.1234 on 2 and 51 DF, p-value: 0.8842
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 0.02892 0.06717 0.430 0.66865
## SIUrge_resid.l1 0.40370 0.11916 3.388 0.00136 **
## const -0.02717 0.07273 -0.374 0.71024
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5342 on 51 degrees of freedom
## Multiple R-Squared: 0.1875, Adjusted R-squared: 0.1556
## F-statistic: 5.884 on 2 and 51 DF, p-value: 0.005022
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.23552 0.04066
## SIUrge_resid 0.04066 0.28536
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.00000 0.06848
## SIUrge_resid 0.06848 1.00000pdat23.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 0.17897, df1 = 1, df2 = 102, p-value = 0.6732summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: 161.605
## Roots of the characteristic polynomial:
## 0.6685 0.4071
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -6.667e-01 1.042e-01 -6.399 4.85e-08 ***
## SIUrge_resid.l1 -5.488e-04 1.297e-03 -0.423 0.674
## const -8.372e-07 7.918e-04 -0.001 0.999
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.005819 on 51 degrees of freedom
## Multiple R-Squared: 0.4464, Adjusted R-squared: 0.4247
## F-statistic: 20.56 on 2 and 51 DF, p-value: 2.83e-07
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -3.55637 9.56959 -0.372 0.71171
## SIUrge_resid.l1 0.40533 0.11916 3.402 0.00131 **
## const -0.02820 0.07273 -0.388 0.69986
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5344 on 51 degrees of freedom
## Multiple R-Squared: 0.1867, Adjusted R-squared: 0.1548
## F-statistic: 5.855 on 2 and 51 DF, p-value: 0.005141
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 3.386e-05 -5.644e-05
## SIUrge_resid -5.644e-05 2.856e-01
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.00000 -0.01815
## SIUrge_resid -0.01815 1.00000pdat23.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 0.043611, df1 = 1, df2 = 102, p-value = 0.835summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -102.442
## Roots of the characteristic polynomial:
## 0.4097 0.01848
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.00322 0.15960 -0.020 0.984
## SIUrge_resid.l1 0.03697 0.17703 0.209 0.835
## const -0.01826 0.10799 -0.169 0.866
##
##
## Residual standard error: 0.7927 on 51 degrees of freedom
## Multiple R-Squared: 0.0008557, Adjusted R-squared: -0.03833
## F-statistic: 0.02184 on 2 and 51 DF, p-value: 0.9784
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.17041 0.10507 1.622 0.11099
## SIUrge_resid.l1 0.39445 0.11655 3.384 0.00138 **
## const -0.03366 0.07110 -0.473 0.63794
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5219 on 51 degrees of freedom
## Multiple R-Squared: 0.2245, Adjusted R-squared: 0.1941
## F-statistic: 7.383 on 2 and 51 DF, p-value: 0.001528
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 0.62838 0.01854
## SIUrge_resid 0.01854 0.27234
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.00000 0.04481
## SIUrge_resid 0.04481 1.00000pdat23.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 0.60741, df1 = 1, df2 = 102, p-value = 0.4376summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -102.229
## Roots of the characteristic polynomial:
## 0.3725 0.03448
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.006022 0.156731 0.038 0.970
## SIUrge_resid.l1 0.135300 0.173603 0.779 0.439
## const -0.037425 0.105835 -0.354 0.725
##
##
## Residual standard error: 0.7776 on 51 degrees of freedom
## Multiple R-Squared: 0.01177, Adjusted R-squared: -0.02698
## F-statistic: 0.3037 on 2 and 51 DF, p-value: 0.7394
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.07710 0.10732 -0.718 0.47577
## SIUrge_resid.l1 0.40099 0.11887 3.373 0.00142 **
## const -0.02742 0.07247 -0.378 0.70671
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5325 on 51 degrees of freedom
## Multiple R-Squared: 0.1927, Adjusted R-squared: 0.161
## F-statistic: 6.086 on 2 and 51 DF, p-value: 0.004261
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.60472 -0.04471
## SIUrge_resid -0.04471 0.28352
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.000 -0.108
## SIUrge_resid -0.108 1.000pdat23.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 3.4313, df1 = 1, df2 = 102, p-value = 0.06686summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -109.77
## Roots of the characteristic polynomial:
## 0.3482 0.03385
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.03591 0.14801 -0.243 0.8092
## SIUrge_resid.l1 0.37086 0.20020 1.852 0.0698 .
## const -0.01393 0.12126 -0.115 0.9090
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8904 on 51 degrees of freedom
## Multiple R-Squared: 0.06304, Adjusted R-squared: 0.0263
## F-statistic: 1.716 on 2 and 51 DF, p-value: 0.1901
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.07226 0.08838 -0.818 0.417377
## SIUrge_resid.l1 0.41797 0.11955 3.496 0.000986 ***
## const -0.02593 0.07241 -0.358 0.721719
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5317 on 51 degrees of freedom
## Multiple R-Squared: 0.1951, Adjusted R-squared: 0.1635
## F-statistic: 6.18 on 2 and 51 DF, p-value: 0.003952
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 0.792826 0.008282
## SIUrge_resid 0.008282 0.282687
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 0.01749
## SIUrge_resid 0.01749 1.00000pdat23.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 0.030915, df1 = 1, df2 = 102, p-value = 0.8608summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -90.563
## Roots of the characteristic polynomial:
## 0.3993 0.3993
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.39514 0.10906 3.623 0.00067 ***
## SIUrge_resid.l1 -0.02582 0.14684 -0.176 0.86113
## const -0.01484 0.08988 -0.165 0.86949
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6575 on 51 degrees of freedom
## Multiple R-Squared: 0.2047, Adjusted R-squared: 0.1735
## F-statistic: 6.564 on 2 and 51 DF, p-value: 0.002906
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.13775 0.08664 1.590 0.11806
## SIUrge_resid.l1 0.39456 0.11666 3.382 0.00139 **
## const -0.01747 0.07140 -0.245 0.80765
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5224 on 51 degrees of freedom
## Multiple R-Squared: 0.223, Adjusted R-squared: 0.1926
## F-statistic: 7.32 on 2 and 51 DF, p-value: 0.001605
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.43231 0.08922
## SIUrge_resid 0.08922 0.27287
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.0000 0.2598
## SIUrge_resid 0.2598 1.0000pdat23.2<-c("Efficacy_resid", "SIUrge_resid")
pdat23.2<-pdat23[pdat23.2]
coping_var=VAR(pdat23.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 3.8951, df1 = 1, df2 = 102, p-value = 0.05113summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -85.313
## Roots of the characteristic polynomial:
## 0.4757 0.4757
## Call:
## VAR(y = pdat23.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.28359 0.12299 2.306 0.0252 *
## SIUrge_resid.l1 -0.28429 0.14405 -1.974 0.0539 .
## const -0.01335 0.08772 -0.152 0.8796
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6436 on 51 degrees of freedom
## Multiple R-Squared: 0.1652, Adjusted R-squared: 0.1325
## F-statistic: 5.047 on 2 and 51 DF, p-value: 0.01001
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.35501 0.08938 3.972 0.000225 ***
## SIUrge_resid.l1 0.44201 0.10468 4.222 9.96e-05 ***
## const -0.01352 0.06375 -0.212 0.832894
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.4677 on 51 degrees of freedom
## Multiple R-Squared: 0.3772, Adjusted R-squared: 0.3527
## F-statistic: 15.44 on 2 and 51 DF, p-value: 5.706e-06
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.414167 0.005432
## SIUrge_resid 0.005432 0.218734
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.00000 0.01805
## SIUrge_resid 0.01805 1.00000230
Specifying the Data Structure for imputation
MImodel = pdat28[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])Person 28: Imputation
m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 591k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat28.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat28.1<-pdat28.imp[vars]
pdat28.2<- do.call(rbind, apply(pdat28.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat28.3<-pdat28.imp[vars]
pdat28.4 <- do.call(rbind, apply(pdat28.3, 1, function(x) {rbind(na.df, x)}))
pdat28.imp<-cbind(pdat28.4, pdat28.2)
pdat28.imp$Day<-c(1:56)Creating splines
pdat28.imp<-data.frame(na.spline(pdat28.imp))
pdat28.imp<-round(pdat28.imp)
pdat28.imp$SIUrge.imp[pdat28.imp$SIUrge.imp>7]<-7
pdat28.imp$SIUrge.imp[pdat28.imp$SIUrge.imp<0]<-0
pdat28.imp$Self_Efficacy.imp[pdat28.imp$Self_Efficacy.imp>10]<-10
pdat28.imp$Self_Efficacy.imp[pdat28.imp$Self_Efficacy.imp<0]<-0pdat28.imp <- pdat28.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat28.imp[cols] <- lapply(pdat28.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat28, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat28.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting standardized residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat28.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_talkMH.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_TalkMH_resid<-as.numeric(rstandard(mod3))
mod4<-glm(all_coping_any.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_any_resid<-as.numeric(rstandard(mod4))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_dis_rel_resid <-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat28.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod9<-glm(all_coping_talkfriend.imp~Day, data=pdat28.imp, family=binomial(link="logit"))
Coping_TalkFriend_resid<-as.numeric(rstandard(mod9))
mod10<-lm(SIUrge.imp~Day, data=pdat28.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat28.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat28<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_any_resid, Coping_dis_rel_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Person 28: Calculating Difference Scores
attach(pdat28)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat23:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat21:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat20:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat13:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_TalkMH_resid, Coping_Thinking_resid, Coping_Thought_resid,
## Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_TalkFriend_resid,
## Coping_Thinking_resid, Coping_Thought_resid, Efficacy_resid,
## SIUrge_residCoping_TalkFamily_resid=diff(Coping_TalkFamily_resid)
Coping_TalkMH_resid = diff(Coping_TalkMH_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_TalkFriend_resid = diff(Coping_TalkFriend_resid)
Coping_any_resid = diff(Coping_any_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat28<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_TalkMH_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_TalkFriend_resid, Coping_any_resid, Coping_dis_rel_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat28$day<-c(1:55)Person 28: Same Day of Models of SI Urge Predicting Changes in Coping
pdat28.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 1.4668, df1 = 1, df2 = 102, p-value = 0.2287summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -98.757
## Roots of the characteristic polynomial:
## 0.3576 0.3576
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.37762 0.09421 4.008 0.0002 ***
## SIUrge_resid.l1 -0.09461 0.07812 -1.211 0.2314
## const 0.01116 0.06556 0.170 0.8655
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.4776 on 51 degrees of freedom
## Multiple R-Squared: 0.2518, Adjusted R-squared: 0.2224
## F-statistic: 8.58 on 2 and 51 DF, p-value: 0.0006136
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.130542 0.159620 0.818 0.4173
## SIUrge_resid.l1 0.306005 0.132357 2.312 0.0249 *
## const -0.008072 0.111077 -0.073 0.9424
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8092 on 51 degrees of freedom
## Multiple R-Squared: 0.1081, Adjusted R-squared: 0.07312
## F-statistic: 3.09 on 2 and 51 DF, p-value: 0.05409
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.2281 0.0188
## SIUrge_resid 0.0188 0.6548
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.00000 0.04865
## SIUrge_resid 0.04865 1.00000pdat28.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 0.070255, df1 = 1, df2 = 102, p-value = 0.7915summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -145.451
## Roots of the characteristic polynomial:
## 0.3085 0.02071
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.006763 0.141243 -0.048 0.962
## SIUrge_resid.l1 -0.050018 0.188707 -0.265 0.792
## const -0.036331 0.155757 -0.233 0.816
##
##
## Residual standard error: 1.144 on 51 degrees of freedom
## Multiple R-Squared: 0.001378, Adjusted R-squared: -0.03778
## F-statistic: 0.0352 on 2 and 51 DF, p-value: 0.9654
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.087887 0.099806 -0.881 0.3827
## SIUrge_resid.l1 0.294517 0.133345 2.209 0.0317 *
## const 0.000731 0.110062 0.007 0.9947
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8084 on 51 degrees of freedom
## Multiple R-Squared: 0.1099, Adjusted R-squared: 0.07503
## F-statistic: 3.149 on 2 and 51 DF, p-value: 0.05132
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.309 -0.1230
## SIUrge_resid -0.123 0.6534
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.000 -0.133
## SIUrge_resid -0.133 1.000pdat28.2<-c("Coping_TalkMH_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkMH_resid
##
## data: VAR object coping_var
## F-Test = 4.1118, df1 = 1, df2 = 102, p-value = 0.04519summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkMH_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -145.593
## Roots of the characteristic polynomial:
## 0.2355 0.2355
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkMH_resid:
## ====================================================
## Coping_TalkMH_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.05736 0.13750 -0.417 0.6783
## SIUrge_resid.l1 0.40062 0.19757 2.028 0.0478 *
## const -0.04696 0.16128 -0.291 0.7721
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.184 on 51 degrees of freedom
## Multiple R-Squared: 0.07461, Adjusted R-squared: 0.03832
## F-statistic: 2.056 on 2 and 51 DF, p-value: 0.1384
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkMH_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkMH_resid.l1 -0.190795 0.090712 -2.103 0.04039 *
## SIUrge_resid.l1 0.365505 0.130338 2.804 0.00712 **
## const -0.004545 0.106398 -0.043 0.96609
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7813 on 51 degrees of freedom
## Multiple R-Squared: 0.1685, Adjusted R-squared: 0.1359
## F-statistic: 5.168 on 2 and 51 DF, p-value: 0.00904
##
##
##
## Covariance matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.4025 0.1083
## SIUrge_resid 0.1083 0.6104
##
## Correlation matrix of residuals:
## Coping_TalkMH_resid SIUrge_resid
## Coping_TalkMH_resid 1.000 0.117
## SIUrge_resid 0.117 1.000pdat28.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 4.2159, df1 = 1, df2 = 102, p-value = 0.04261summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -149.743
## Roots of the characteristic polynomial:
## 0.1418 0.1418
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.05549 0.13728 -0.404 0.6877
## SIUrge_resid.l1 -0.42424 0.20662 -2.053 0.0452 *
## const 0.01319 0.16867 0.078 0.9380
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.239 on 51 degrees of freedom
## Multiple R-Squared: 0.07635, Adjusted R-squared: 0.04013
## F-statistic: 2.108 on 2 and 51 DF, p-value: 0.1319
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.091567 0.089297 1.025 0.3100
## SIUrge_resid.l1 0.337683 0.134400 2.513 0.0152 *
## const 0.002731 0.109719 0.025 0.9802
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8062 on 51 degrees of freedom
## Multiple R-Squared: 0.1147, Adjusted R-squared: 0.07993
## F-statistic: 3.302 on 2 and 51 DF, p-value: 0.04481
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.536 -0.117
## SIUrge_resid -0.117 0.650
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.0000 -0.1171
## SIUrge_resid -0.1171 1.0000pdat28.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 0.45553, df1 = 1, df2 = 102, p-value = 0.5012summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -134.199
## Roots of the characteristic polynomial:
## 0.2889 0.01862
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.01001 0.13983 -0.072 0.943
## SIUrge_resid.l1 0.10167 0.15064 0.675 0.503
## const -0.03556 0.12515 -0.284 0.777
##
##
## Residual standard error: 0.919 on 51 degrees of freedom
## Multiple R-Squared: 0.00886, Adjusted R-squared: -0.03001
## F-statistic: 0.228 on 2 and 51 DF, p-value: 0.797
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.0841715 0.1233678 -0.682 0.4981
## SIUrge_resid.l1 0.3175193 0.1329054 2.389 0.0206 *
## const 0.0008837 0.1104208 0.008 0.9936
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8108 on 51 degrees of freedom
## Multiple R-Squared: 0.1046, Adjusted R-squared: 0.06946
## F-statistic: 2.978 on 2 and 51 DF, p-value: 0.05981
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.84449 0.03769
## SIUrge_resid 0.03769 0.65737
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.00000 0.05059
## SIUrge_resid 0.05059 1.00000pdat28.2<-c("Coping_TalkFriend_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFriend_resid
##
## data: VAR object coping_var
## F-Test = 3.7202, df1 = 1, df2 = 102, p-value = 0.05654summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFriend_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -137.204
## Roots of the characteristic polynomial:
## 0.2042 0.2042
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFriend_resid:
## ========================================================
## Coping_TalkFriend_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 -0.01837 0.13545 -0.136 0.8927
## SIUrge_resid.l1 -0.31090 0.16119 -1.929 0.0593 .
## const -0.02692 0.13401 -0.201 0.8416
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9844 on 51 degrees of freedom
## Multiple R-Squared: 0.06799, Adjusted R-squared: 0.03144
## F-statistic: 1.86 on 2 and 51 DF, p-value: 0.166
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFriend_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFriend_resid.l1 0.153130 0.110000 1.392 0.1699
## SIUrge_resid.l1 0.321866 0.130904 2.459 0.0174 *
## const 0.008078 0.108834 0.074 0.9411
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7994 on 51 degrees of freedom
## Multiple R-Squared: 0.1295, Adjusted R-squared: 0.09534
## F-statistic: 3.793 on 2 and 51 DF, p-value: 0.02913
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 0.96899 0.01888
## SIUrge_resid 0.01888 0.63908
##
## Correlation matrix of residuals:
## Coping_TalkFriend_resid SIUrge_resid
## Coping_TalkFriend_resid 1.00000 0.02399
## SIUrge_resid 0.02399 1.00000pdat28.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 13.414, df1 = 1, df2 = 102, p-value = 0.0003981summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -148.561
## Roots of the characteristic polynomial:
## 0.1695 0.08503
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.067418 0.125974 -0.535 0.594855
## SIUrge_resid.l1 -0.723604 0.197573 -3.662 0.000594 ***
## const 0.008718 0.162757 0.054 0.957490
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.196 on 51 degrees of freedom
## Multiple R-Squared: 0.2082, Adjusted R-squared: 0.1772
## F-statistic: 6.707 on 2 and 51 DF, p-value: 0.002595
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.04990 0.08550 0.584 0.5620
## SIUrge_resid.l1 0.32191 0.13410 2.400 0.0201 *
## const 0.00356 0.11047 0.032 0.9744
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8118 on 51 degrees of freedom
## Multiple R-Squared: 0.1024, Adjusted R-squared: 0.06719
## F-statistic: 2.909 on 2 and 51 DF, p-value: 0.06363
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.4303521 -0.0009061
## SIUrge_resid -0.0009061 0.6589672
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.0000000 -0.0009333
## SIUrge_resid -0.0009333 1.0000000pdat28.2<-c("Coping_any_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_any_resid
##
## data: VAR object coping_var
## F-Test = 9.8358, df1 = 1, df2 = 102, p-value = 0.002237summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_any_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -127.2
## Roots of the characteristic polynomial:
## 0.4404 0.4404
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_any_resid:
## =================================================
## Coping_any_resid = Coping_any_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_any_resid.l1 -0.04429 0.13664 -0.324 0.74717
## SIUrge_resid.l1 -0.48258 0.15388 -3.136 0.00284 **
## const 0.06303 0.12747 0.494 0.62311
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.9365 on 51 degrees of freedom
## Multiple R-Squared: 0.1617, Adjusted R-squared: 0.1288
## F-statistic: 4.918 on 2 and 51 DF, p-value: 0.01114
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_any_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_any_resid.l1 0.434978 0.102037 4.263 8.72e-05 ***
## SIUrge_resid.l1 0.360940 0.114905 3.141 0.0028 **
## const -0.002706 0.095184 -0.028 0.9774
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6994 on 51 degrees of freedom
## Multiple R-Squared: 0.3338, Adjusted R-squared: 0.3077
## F-statistic: 12.78 on 2 and 51 DF, p-value: 3.178e-05
##
##
##
## Covariance matrix of residuals:
## Coping_any_resid SIUrge_resid
## Coping_any_resid 0.87710 0.04135
## SIUrge_resid 0.04135 0.48909
##
## Correlation matrix of residuals:
## Coping_any_resid SIUrge_resid
## Coping_any_resid 1.00000 0.06313
## SIUrge_resid 0.06313 1.00000pdat28.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 4.5783, df1 = 1, df2 = 102, p-value = 0.03476summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -111.248
## Roots of the characteristic polynomial:
## 0.3558 0.3558
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.298808 0.120254 2.485 0.0163 *
## SIUrge_resid.l1 -0.220695 0.103143 -2.140 0.0372 *
## const 0.004975 0.083603 0.060 0.9528
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6136 on 51 degrees of freedom
## Multiple R-Squared: 0.2154, Adjusted R-squared: 0.1847
## F-statistic: 7.001 on 2 and 51 DF, p-value: 0.002057
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.1205954 0.1587138 0.760 0.4509
## SIUrge_resid.l1 0.3346561 0.1361312 2.458 0.0174 *
## const -0.0001571 0.1103415 -0.001 0.9989
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8099 on 51 degrees of freedom
## Multiple R-Squared: 0.1065, Adjusted R-squared: 0.07147
## F-statistic: 3.04 on 2 and 51 DF, p-value: 0.05659
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.3766 -0.1017
## SIUrge_resid -0.1017 0.6559
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.0000 -0.2047
## SIUrge_resid -0.2047 1.0000pdat28.2<-c("Efficacy_resid", "SIUrge_resid")
pdat28.2<-pdat28[pdat28.2]
coping_var=VAR(pdat28.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 26.244, df1 = 1, df2 = 102, p-value = 1.428e-06summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -99.151
## Roots of the characteristic polynomial:
## 0.491 0.491
## Call:
## VAR(y = pdat28.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.308556 0.095404 3.234 0.00214 **
## SIUrge_resid.l1 -0.435990 0.085106 -5.123 4.66e-06 ***
## const -0.005253 0.069058 -0.076 0.93966
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.5071 on 51 degrees of freedom
## Multiple R-Squared: 0.4778, Adjusted R-squared: 0.4574
## F-statistic: 23.33 on 2 and 51 DF, p-value: 6.371e-08
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.291340 0.147708 1.972 0.0540 .
## SIUrge_resid.l1 0.369659 0.131765 2.805 0.0071 **
## const -0.004315 0.106918 -0.040 0.9680
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.7851 on 51 degrees of freedom
## Multiple R-Squared: 0.1604, Adjusted R-squared: 0.1275
## F-statistic: 4.873 on 2 and 51 DF, p-value: 0.01157
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.25713 -0.08536
## SIUrge_resid -0.08536 0.61635
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 -0.2144
## SIUrge_resid -0.2144 1.0000df <- pdat28.imp %>%
dplyr::select(Day, SIUrge.imp, Self_Efficacy.imp) %>%
tidyr::gather(key = "variable", value = "value", -Day)
a<-ggplot(df, aes(x = Day, y = value)) +
geom_line(aes(linetype = variable), size = 1) + labs(y="Value", x = "Day of Study") + theme_bw()
a<-a+scale_linetype_manual(values=c("dashed", "solid"), name="Variable", labels=c("Self-Efficacy", "Suicidal Urge"))
jpeg("Person 28.SUM.jpeg", res=300, height=6, width=9, units="in")
a
dev.off()## quartz_off_screen
## 2336
Specifying the Data Structure for imputation
MImodel = pdat34[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg* all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg* all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_copingthought all_coping_thinking all_coping_dis_rel_combined coping_sum coping_sum_3avg all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 426k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat34.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat34.1<-pdat34.imp[vars]
pdat34.2<- do.call(rbind, apply(pdat34.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat34.3<-pdat34.imp[vars]
pdat34.4 <- do.call(rbind, apply(pdat34.3, 1, function(x) {rbind(na.df, x)}))
pdat34.imp<-cbind(pdat34.4, pdat34.2)
pdat34.imp$Day<-c(1:56)Creating splines
pdat34.imp<-data.frame(na.spline(pdat34.imp))
pdat34.imp<-round(pdat34.imp)
pdat34.imp$SIUrge.imp[pdat34.imp$SIUrge.imp>7]<-7
pdat34.imp$SIUrge.imp[pdat34.imp$SIUrge.imp<0]<-0
pdat34.imp$Self_Efficacy.imp[pdat34.imp$Self_Efficacy.imp>10]<-10
pdat34.imp$Self_Efficacy.imp[pdat34.imp$Self_Efficacy.imp<0]<-0pdat34.imp <- pdat34.imp %>%
mutate_at(c(cols),list(~recode(., `-3`=0,`-2`=0,`-1`=0,`2`= 1,`3`=1)))
cols <- c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp")
pdat34.imp[cols] <- lapply(pdat34.imp[cols], factor) Comparing pre vs post splines
a<-ggplot(data = pdat34, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
b<-ggplot(data = pdat34.imp, aes(x = Day, y = SIUrge.imp))+
geom_line(color = "#00AFBB", size = 2)
ggarrange(a, b + rremove("x.text"),
ncol = 1, nrow = 2)
Extracting standardized residuals
mod1<-lm(coping_sum_3avg.imp~Day, data=pdat34.imp)
Coping_sum_3avg_resid = as.numeric(rstandard(mod1))
mod2<-glm(all_coping_talkfamily.imp~Day, data=pdat34.imp, family=binomial(link="logit"))
Coping_TalkFamily_resid<-as.numeric(rstandard(mod2))
mod3<-glm(all_coping_any.imp~Day, data=pdat34.imp, family=binomial(link="logit"))
Coping_any_resid<-as.numeric(rstandard(mod3))
mod5<-glm(all_coping_dis_rel_combined.imp~Day, data=pdat34.imp, family=binomial(link="logit"))
Coping_dis_rel_resid<-as.numeric(rstandard(mod5))
mod6<-glm(all_coping_copingthought.imp~Day, data=pdat34.imp, family=binomial(link="logit"))
Coping_Thought_resid<-as.numeric(rstandard(mod6))
mod7<-glm(all_coping_thinking.imp~Day, data=pdat34.imp, family=binomial(link="logit"))
Coping_Thinking_resid<-as.numeric(rstandard(mod7))
mod8<-lm(coping_sum.imp~Day, data=pdat34.imp)
Coping_sum_resid<-as.numeric(rstandard(mod8))
mod10<-lm(SIUrge.imp~Day, data=pdat34.imp)
SIUrge_resid<-as.numeric(rstandard(mod10))
mod11<-lm(Self_Efficacy.imp~Day, data=pdat34.imp)
Efficacy_resid<-as.numeric(rstandard(mod11))
pdat34<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_any_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))Person 34: Calculating Difference Scores
attach(pdat34)## The following objects are masked _by_ .GlobalEnv:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat28:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat23:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat21:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat20:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat13:
##
## Coping_dis_rel_resid, Coping_sum_3avg_resid, Coping_sum_resid,
## Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_resid## The following objects are masked from pdat11:
##
## Coping_any_resid, Coping_dis_rel_resid, Coping_sum_3avg_resid,
## Coping_sum_resid, Coping_TalkFamily_resid, Coping_Thinking_resid,
## Coping_Thought_resid, Efficacy_resid, SIUrge_residCoping_TalkFamily_resid = diff(Coping_TalkFamily_resid)
Coping_dis_rel_resid = diff(Coping_dis_rel_resid)
Coping_Thought_resid = diff(Coping_Thought_resid)
Coping_Thinking_resid = diff(Coping_Thinking_resid)
Coping_any_resid = diff(Coping_any_resid)
Coping_sum_resid = diff(Coping_sum_resid)
SIUrge_resid = diff(SIUrge_resid)
Efficacy_resid = diff(Efficacy_resid)
Coping_sum_3avg_resid = diff(Coping_sum_3avg_resid)
pdat34<-as.data.frame(cbind(Coping_TalkFamily_resid, Coping_dis_rel_resid, Coping_Thought_resid, Coping_Thinking_resid, Coping_any_resid, Coping_sum_resid, SIUrge_resid, Efficacy_resid, Coping_sum_3avg_resid))
pdat34$day<-c(1:55)##Person 34: Same Day Models of SI Urge Predicting Changes in Coping ##
pdat34.2<-c("Coping_sum_3avg_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_3avg_resid
##
## data: VAR object coping_var
## F-Test = 2.0992, df1 = 1, df2 = 102, p-value = 0.1504summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_3avg_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -101.32
## Roots of the characteristic polynomial:
## 0.5009 0.0289
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_3avg_resid:
## ======================================================
## Coping_sum_3avg_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 -0.02910 0.11572 -0.251 0.802
## SIUrge_resid.l1 -0.17898 0.12353 -1.449 0.153
## const 0.06026 0.08728 0.690 0.493
##
##
## Residual standard error: 0.6402 on 51 degrees of freedom
## Multiple R-Squared: 0.03954, Adjusted R-squared: 0.001874
## F-statistic: 1.05 on 2 and 51 DF, p-value: 0.3575
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_3avg_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_3avg_resid.l1 0.0005893 0.1150575 0.005 0.995933
## SIUrge_resid.l1 0.5011295 0.1228158 4.080 0.000158 ***
## const -0.0213160 0.0867725 -0.246 0.806936
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6365 on 51 degrees of freedom
## Multiple R-Squared: 0.251, Adjusted R-squared: 0.2217
## F-statistic: 8.547 on 2 and 51 DF, p-value: 0.0006293
##
##
##
## Covariance matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 0.40984 -0.04688
## SIUrge_resid -0.04688 0.40513
##
## Correlation matrix of residuals:
## Coping_sum_3avg_resid SIUrge_resid
## Coping_sum_3avg_resid 1.000 -0.115
## SIUrge_resid -0.115 1.000pdat34.2<-c("Coping_TalkFamily_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_TalkFamily_resid
##
## data: VAR object coping_var
## F-Test = 1.4202, df1 = 1, df2 = 102, p-value = 0.2361summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_TalkFamily_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -135.493
## Roots of the characteristic polynomial:
## 0.5009 0.03685
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_TalkFamily_resid:
## ========================================================
## Coping_TalkFamily_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 -0.0498782 0.1397296 -0.357 0.723
## SIUrge_resid.l1 -0.2960602 0.2484319 -1.192 0.239
## const 0.0003464 0.1698802 0.002 0.998
##
##
## Residual standard error: 1.245 on 51 degrees of freedom
## Multiple R-Squared: 0.02709, Adjusted R-squared: -0.01106
## F-statistic: 0.7101 on 2 and 51 DF, p-value: 0.4964
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_TalkFamily_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_TalkFamily_resid.l1 0.02423 0.07136 0.340 0.735557
## SIUrge_resid.l1 0.51394 0.12688 4.051 0.000174 ***
## const -0.02001 0.08676 -0.231 0.818513
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6358 on 51 degrees of freedom
## Multiple R-Squared: 0.2527, Adjusted R-squared: 0.2234
## F-statistic: 8.624 on 2 and 51 DF, p-value: 0.0005941
##
##
##
## Covariance matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.5498 -0.2134
## SIUrge_resid -0.2134 0.4042
##
## Correlation matrix of residuals:
## Coping_TalkFamily_resid SIUrge_resid
## Coping_TalkFamily_resid 1.0000 -0.2696
## SIUrge_resid -0.2696 1.0000pdat34.2<-c("Coping_dis_rel_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_dis_rel_resid
##
## data: VAR object coping_var
## F-Test = 4.7873, df1 = 1, df2 = 102, p-value = 0.03095summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_dis_rel_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -125.106
## Roots of the characteristic polynomial:
## 0.474 0.03048
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_dis_rel_resid:
## =====================================================
## Coping_dis_rel_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 -0.11502 0.14413 -0.798 0.4285
## SIUrge_resid.l1 -0.46429 0.21220 -2.188 0.0333 *
## const -0.02614 0.14155 -0.185 0.8542
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 1.038 on 51 degrees of freedom
## Multiple R-Squared: 0.08581, Adjusted R-squared: 0.04996
## F-statistic: 2.394 on 2 and 51 DF, p-value: 0.1015
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_dis_rel_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_dis_rel_resid.l1 0.10726 0.08710 1.231 0.224
## SIUrge_resid.l1 0.55857 0.12824 4.356 6.41e-05 ***
## const -0.01836 0.08554 -0.215 0.831
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6272 on 51 degrees of freedom
## Multiple R-Squared: 0.2727, Adjusted R-squared: 0.2441
## F-statistic: 9.559 on 2 and 51 DF, p-value: 0.0002981
##
##
##
## Covariance matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.0773 -0.1687
## SIUrge_resid -0.1687 0.3934
##
## Correlation matrix of residuals:
## Coping_dis_rel_resid SIUrge_resid
## Coping_dis_rel_resid 1.0000 -0.2591
## SIUrge_resid -0.2591 1.0000pdat34.2<-c("Coping_Thought_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thought_resid
##
## data: VAR object coping_var
## F-Test = 0.20878, df1 = 1, df2 = 102, p-value = 0.6487summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thought_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -110.948
## Roots of the characteristic polynomial:
## 0.5189 0.01279
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thought_resid:
## =====================================================
## Coping_Thought_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 -0.02514 0.14652 -0.172 0.864
## SIUrge_resid.l1 -0.07345 0.16075 -0.457 0.650
## const -0.01362 0.10983 -0.124 0.902
##
##
## Residual standard error: 0.8052 on 51 degrees of freedom
## Multiple R-Squared: 0.004102, Adjusted R-squared: -0.03495
## F-statistic: 0.105 on 2 and 51 DF, p-value: 0.9005
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thought_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thought_resid.l1 0.09143 0.11511 0.794 0.430700
## SIUrge_resid.l1 0.53120 0.12629 4.206 0.000105 ***
## const -0.01912 0.08628 -0.222 0.825536
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6326 on 51 degrees of freedom
## Multiple R-Squared: 0.2602, Adjusted R-squared: 0.2312
## F-statistic: 8.968 on 2 and 51 DF, p-value: 0.0004599
##
##
##
## Covariance matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 0.6484 -0.1595
## SIUrge_resid -0.1595 0.4002
##
## Correlation matrix of residuals:
## Coping_Thought_resid SIUrge_resid
## Coping_Thought_resid 1.0000 -0.3131
## SIUrge_resid -0.3131 1.0000pdat34.2<-c("Coping_Thinking_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_Thinking_resid
##
## data: VAR object coping_var
## F-Test = 6.3023, df1 = 1, df2 = 102, p-value = 0.01363summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_Thinking_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -110.201
## Roots of the characteristic polynomial:
## 0.4757 0.04035
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_Thinking_resid:
## ======================================================
## Coping_Thinking_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 -0.1304068 0.1319569 -0.988 0.3277
## SIUrge_resid.l1 -0.4172948 0.1662244 -2.510 0.0153 *
## const 0.0004598 0.1096460 0.004 0.9967
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8029 on 51 degrees of freedom
## Multiple R-Squared: 0.11, Adjusted R-squared: 0.07508
## F-statistic: 3.151 on 2 and 51 DF, p-value: 0.05125
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_Thinking_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_Thinking_resid.l1 0.13080 0.10299 1.270 0.210
## SIUrge_resid.l1 0.56573 0.12973 4.361 6.31e-05 ***
## const -0.01502 0.08558 -0.176 0.861
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6267 on 51 degrees of freedom
## Multiple R-Squared: 0.274, Adjusted R-squared: 0.2455
## F-statistic: 9.623 on 2 and 51 DF, p-value: 0.0002845
##
##
##
## Covariance matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 0.6447 -0.1598
## SIUrge_resid -0.1598 0.3927
##
## Correlation matrix of residuals:
## Coping_Thinking_resid SIUrge_resid
## Coping_Thinking_resid 1.0000 -0.3175
## SIUrge_resid -0.3175 1.0000pdat34.2<-c("Coping_any_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_any_resid
##
## data: VAR object coping_var
## F-Test = 5.5077, df1 = 1, df2 = 102, p-value = 0.02087summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_any_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -112.714
## Roots of the characteristic polynomial:
## 0.4732 0.04254
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_any_resid:
## =================================================
## Coping_any_resid = Coping_any_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_any_resid.l1 -0.14076 0.14773 -0.953 0.3452
## SIUrge_resid.l1 -0.40816 0.17392 -2.347 0.0229 *
## const -0.03223 0.11395 -0.283 0.7784
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.8353 on 51 degrees of freedom
## Multiple R-Squared: 0.09747, Adjusted R-squared: 0.06207
## F-statistic: 2.754 on 2 and 51 DF, p-value: 0.07316
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_any_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_any_resid.l1 0.14774 0.11066 1.335 0.188
## SIUrge_resid.l1 0.57144 0.13027 4.386 5.79e-05 ***
## const -0.01694 0.08536 -0.198 0.844
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6257 on 51 degrees of freedom
## Multiple R-Squared: 0.2763, Adjusted R-squared: 0.2479
## F-statistic: 9.737 on 2 and 51 DF, p-value: 0.0002621
##
##
##
## Covariance matrix of residuals:
## Coping_any_resid SIUrge_resid
## Coping_any_resid 0.6977 -0.1525
## SIUrge_resid -0.1525 0.3915
##
## Correlation matrix of residuals:
## Coping_any_resid SIUrge_resid
## Coping_any_resid 1.0000 -0.2917
## SIUrge_resid -0.2917 1.0000pdat34.2<-c("Coping_sum_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause
## Coping_sum_resid
##
## data: VAR object coping_var
## F-Test = 6.7067, df1 = 1, df2 = 102, p-value = 0.01101summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Coping_sum_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -99.476
## Roots of the characteristic polynomial:
## 0.3881 0.3881
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Coping_sum_resid:
## =================================================
## Coping_sum_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.107666 0.138956 0.775 0.4420
## SIUrge_resid.l1 -0.472881 0.182598 -2.590 0.0125 *
## const 0.004823 0.105726 0.046 0.9638
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.774 on 51 degrees of freedom
## Multiple R-Squared: 0.2256, Adjusted R-squared: 0.1952
## F-statistic: 7.428 on 2 and 51 DF, p-value: 0.001475
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Coping_sum_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Coping_sum_resid.l1 0.17376 0.11165 1.556 0.126
## SIUrge_resid.l1 0.63585 0.14671 4.334 6.89e-05 ***
## const -0.01307 0.08495 -0.154 0.878
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6219 on 51 degrees of freedom
## Multiple R-Squared: 0.285, Adjusted R-squared: 0.2569
## F-statistic: 10.16 on 2 and 51 DF, p-value: 0.0001928
##
##
##
## Covariance matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 0.5991 -0.2805
## SIUrge_resid -0.2805 0.3868
##
## Correlation matrix of residuals:
## Coping_sum_resid SIUrge_resid
## Coping_sum_resid 1.0000 -0.5827
## SIUrge_resid -0.5827 1.0000pdat34.2<-c("Efficacy_resid", "SIUrge_resid")
pdat34.2<-pdat34[pdat34.2]
coping_var=VAR(pdat34.2,p=1, type="const")
causality(coping_var, cause="SIUrge_resid")$Granger##
## Granger causality H0: SIUrge_resid do not Granger-cause Efficacy_resid
##
## data: VAR object coping_var
## F-Test = 11.411, df1 = 1, df2 = 102, p-value = 0.001035summary(coping_var)##
## VAR Estimation Results:
## =========================
## Endogenous variables: Efficacy_resid, SIUrge_resid
## Deterministic variables: const
## Sample size: 54
## Log Likelihood: -91.356
## Roots of the characteristic polynomial:
## 0.3784 0.3784
## Call:
## VAR(y = pdat34.2, p = 1, type = "const")
##
##
## Estimation results for equation Efficacy_resid:
## ===============================================
## Efficacy_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.12358 0.12121 1.020 0.31276
## SIUrge_resid.l1 -0.46372 0.13728 -3.378 0.00141 **
## const 0.01706 0.08366 0.204 0.83925
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6131 on 51 degrees of freedom
## Multiple R-Squared: 0.3036, Adjusted R-squared: 0.2762
## F-statistic: 11.11 on 2 and 51 DF, p-value: 9.856e-05
##
##
## Estimation results for equation SIUrge_resid:
## =============================================
## SIUrge_resid = Efficacy_resid.l1 + SIUrge_resid.l1 + const
##
## Estimate Std. Error t value Pr(>|t|)
## Efficacy_resid.l1 0.15128 0.12403 1.220 0.228178
## SIUrge_resid.l1 0.59118 0.14047 4.209 0.000104 ***
## const -0.01682 0.08561 -0.196 0.845012
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
##
## Residual standard error: 0.6274 on 51 degrees of freedom
## Multiple R-Squared: 0.2723, Adjusted R-squared: 0.2437
## F-statistic: 9.54 on 2 and 51 DF, p-value: 0.0003023
##
##
##
## Covariance matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 0.3759 -0.1863
## SIUrge_resid -0.1863 0.3937
##
## Correlation matrix of residuals:
## Efficacy_resid SIUrge_resid
## Efficacy_resid 1.0000 -0.4843
## SIUrge_resid -0.4843 1.0000Imputation and splines for people with less than 5 SI observations
201
Specifying the Data Structure for imputation
MImodel = pdat1[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 482k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat1.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat1.1<-pdat1.imp[vars]
pdat1.2<- do.call(rbind, apply(pdat1.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat1.3<-pdat1.imp[vars]
pdat1.4 <- do.call(rbind, apply(pdat1.3, 1, function(x) {rbind(na.df, x)}))
pdat1.imp<-cbind(pdat1.4, pdat1.2)
pdat1.imp$Day<-c(1:56)Creating splines
pdat1.imp<-data.frame(na.spline(pdat1.imp))
pdat1.imp<-round(pdat1.imp)
pdat1.imp$SIUrge.imp[pdat1.imp$SIUrge.imp>7]<-7
pdat1.imp$SIUrge.imp[pdat1.imp$SIUrge.imp<0]<-0
pdat1.imp$Self_Efficacy.imp[pdat1.imp$Self_Efficacy.imp>10]<-10
pdat1.imp$Self_Efficacy.imp[pdat1.imp$Self_Efficacy.imp<0]<-0206
Specifying the Data Structure for imputation
MImodel = pdat6[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag* Self_Efficacy.lag*
## 1 2 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 1 3 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag* Self_Efficacy.lag*
## 1 4 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag* Self_Efficacy.lag*
## 1 5 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 2 1 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 2 2 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag* Self_Efficacy.lag
## 2 3 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 2 4 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 2 5 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 3 1 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 3 2 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 3 3 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 3 4 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 3 5 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 4 1 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 4 2 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag* Self_Efficacy.lag*
## 4 3 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 4 4 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 4 5 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 5 1 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## 5 2 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 5 3 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 5 4 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg* SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag
## 5 5 all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_crisisline coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_crisisline.lag coping_sum.lag Self_Efficacy.lag*
## * Please inspect the loggedEvents## Warning: Number of logged events: 432k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat6.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat6.1<-pdat6.imp[vars]
pdat6.2<- do.call(rbind, apply(pdat6.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat6.3<-pdat6.imp[vars]
pdat6.4 <- do.call(rbind, apply(pdat6.3, 1, function(x) {rbind(na.df, x)}))
pdat6.imp<-cbind(pdat6.4, pdat6.2)
pdat6.imp$Day<-c(1:56)Creating splines
pdat6.imp<-data.frame(na.spline(pdat6.imp))
pdat6.imp<-round(pdat6.imp)
pdat6.imp$SIUrge.imp[pdat6.imp$SIUrge.imp>7]<-7
pdat6.imp$SIUrge.imp[pdat6.imp$SIUrge.imp<0]<-0
pdat6.imp$Self_Efficacy.imp[pdat6.imp$Self_Efficacy.imp>10]<-10
pdat6.imp$Self_Efficacy.imp[pdat6.imp$Self_Efficacy.imp<0]<-0209 (pdat8)
Specifying the Data Structure for imputation
MImodel = pdat8[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 44k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat8.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat8.1<-pdat8.imp[vars]
pdat8.2<- do.call(rbind, apply(pdat8.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat8.3<-pdat8.imp[vars]
pdat8.4 <- do.call(rbind, apply(pdat8.3, 1, function(x) {rbind(na.df, x)}))
pdat8.imp<-cbind(pdat8.4, pdat8.2)
pdat8.imp$Day<-c(1:56)Creating splines
pdat8.imp<-data.frame(na.spline(pdat8.imp))
pdat8.imp<-round(pdat8.imp)
pdat8.imp$SIUrge.imp[pdat8.imp$SIUrge.imp>7]<-7
pdat8.imp$SIUrge.imp[pdat8.imp$SIUrge.imp<0]<-0
pdat8.imp$Self_Efficacy.imp[pdat8.imp$Self_Efficacy.imp>10]<-10
pdat8.imp$Self_Efficacy.imp[pdat8.imp$Self_Efficacy.imp<0]<-0211 (pdat 10)
Specifying the Data Structure for imputation
MImodel = pdat10[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag* all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum* all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag* Self_Efficacy.lag*
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum all_coping_any SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag*
## * Please inspect the loggedEvents## Warning: Number of logged events: 610k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat10.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat10.1<-pdat10.imp[vars]
pdat10.2<- do.call(rbind, apply(pdat10.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat10.3<-pdat10.imp[vars]
pdat10.4 <- do.call(rbind, apply(pdat10.3, 1, function(x) {rbind(na.df, x)}))
pdat10.imp<-cbind(pdat10.4, pdat10.2)
pdat10.imp$Day<-c(1:56)Creating splines
pdat10.imp<-data.frame(na.spline(pdat10.imp))
pdat10.imp<-round(pdat10.imp)
pdat10.imp$SIUrge.imp[pdat10.imp$SIUrge.imp>7]<-7
pdat10.imp$SIUrge.imp[pdat10.imp$SIUrge.imp<0]<-0
pdat10.imp$Self_Efficacy.imp[pdat10.imp$Self_Efficacy.imp>10]<-10
pdat10.imp$Self_Efficacy.imp[pdat10.imp$Self_Efficacy.imp<0]<-0220 (pdat18)
Specifying the Data Structure for imputation
MImodel = pdat18[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH## Warning: glm.fit: algorithm did not converge## all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH## Warning: glm.fit: algorithm did not converge## all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH## Warning: glm.fit: algorithm did not converge## all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend all_coping_dis_rel_combined coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag all_coping_dis_rel_combined.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 199k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat18.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat18.1<-pdat18.imp[vars]
pdat18.2<- do.call(rbind, apply(pdat18.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat18.3<-pdat18.imp[vars]
pdat18.4 <- do.call(rbind, apply(pdat18.3, 1, function(x) {rbind(na.df, x)}))
pdat18.imp<-cbind(pdat18.4, pdat18.2)
pdat18.imp$Day<-c(1:56)Creating splines
pdat18.imp<-data.frame(na.spline(pdat18.imp))
pdat18.imp<-round(pdat18.imp)
pdat18.imp$SIUrge.imp[pdat18.imp$SIUrge.imp>7]<-7
pdat18.imp$SIUrge.imp[pdat18.imp$SIUrge.imp<0]<-0
pdat18.imp$Self_Efficacy.imp[pdat18.imp$Self_Efficacy.imp>10]<-10
pdat18.imp$Self_Efficacy.imp[pdat18.imp$Self_Efficacy.imp<0]<-0226 (pdat24)
Specifying the Data Structure for imputation
MImodel = pdat24[c(-1,-2, -7, -20)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.numeric(MImodel[,7])
MImodel[,8] = as.numeric(MImodel[,8])
MImodel[,9] = as.factor(MImodel[,9])
MImodel[,10] = as.numeric(MImodel[,10])
MImodel[,11] = as.numeric(MImodel[,11])
MImodel[,12] = as.numeric(MImodel[,12])
MImodel[,13] = as.factor(MImodel[,13])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.numeric(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,21] = as.numeric(MImodel[,21])
MImodel[,22] = as.numeric(MImodel[,22])m = 5
imp = mice(MImodel, m = m)##
## iter imp variable
## 1 1 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 2 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 3 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 4 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 5 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 1 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 2 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 3 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 4 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 5 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 1 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 2 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 3 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 4 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 5 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 1 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 2 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 3 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 4 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 5 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 1 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 2 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 3 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 4 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 5 coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_dis_rel_combined.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag## Warning: Number of logged events: 2k=22
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
coping_sum.imp = data.impute[,7]
coping_sum_3avg.imp = data.impute[,8]
all_coping_any.imp = as.factor(data.impute[,9])
SIUrge.imp = data.impute[,10]
Self_Efficacy.imp = data.impute[,11]
pdat24.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat24.1<-pdat24.imp[vars]
pdat24.2<- do.call(rbind, apply(pdat24.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat24.3<-pdat24.imp[vars]
pdat24.4 <- do.call(rbind, apply(pdat24.3, 1, function(x) {rbind(na.df, x)}))
pdat24.imp<-cbind(pdat24.4, pdat24.2)
pdat24.imp$Day<-c(1:56)Creating splines
pdat24.imp<-data.frame(na.spline(pdat24.imp))
pdat24.imp<-round(pdat24.imp)
pdat24.imp$SIUrge.imp[pdat24.imp$SIUrge.imp>7]<-7
pdat24.imp$SIUrge.imp[pdat24.imp$SIUrge.imp<0]<-0
pdat24.imp$Self_Efficacy.imp[pdat24.imp$Self_Efficacy.imp>10]<-10
pdat24.imp$Self_Efficacy.imp[pdat24.imp$Self_Efficacy.imp<0]<-0229 (pdat27)
Specifying the Data Structure for imputation
MImodel = pdat27[c(-1,-2)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.factor(MImodel[,7])
MImodel[,10] = as.factor(MImodel[,10])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.factor(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,22] = as.factor(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge* Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag*
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag* Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge* Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge Self_Efficacy* coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg* SIUrge* Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge* Self_Efficacy* coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge* Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag*
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking all_coping_talkfriend coping_sum coping_sum_3avg SIUrge Self_Efficacy coping_sum_3avg.lag* all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag all_coping_talkfriend.lag coping_sum.lag SIUrge.lag Self_Efficacy.lag
## * Please inspect the loggedEvents## Warning: Number of logged events: 432k=24
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
all_coping_crisisline.imp = as.factor(data.impute[,7])
coping_sum.imp = data.impute[,8]
coping_sum_3avg.imp = data.impute[,9]
all_coping_any.imp = as.factor(data.impute[,10])
SIUrge.imp = data.impute[,11]
Self_Efficacy.imp = data.impute[,12]
pdat27.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat27.1<-pdat27.imp[vars]
pdat27.2<- do.call(rbind, apply(pdat27.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat27.3<-pdat27.imp[vars]
pdat27.4 <- do.call(rbind, apply(pdat27.3, 1, function(x) {rbind(na.df, x)}))
pdat27.imp<-cbind(pdat27.4, pdat27.2)
pdat27.imp$Day<-c(1:56)Creating splines
pdat27.imp<-data.frame(na.spline(pdat27.imp))
pdat27.imp<-round(pdat27.imp)
pdat27.imp$SIUrge.imp[pdat27.imp$SIUrge.imp>7]<-7
pdat27.imp$SIUrge.imp[pdat27.imp$SIUrge.imp<0]<-0
pdat27.imp$Self_Efficacy.imp[pdat27.imp$Self_Efficacy.imp>10]<-10
pdat27.imp$Self_Efficacy.imp[pdat27.imp$Self_Efficacy.imp<0]<-0233 (pdat31)
Specifying the Data Structure for imputation
MImodel = pdat31[c(-1,-2, -7, -20)]
MImodel[,1] = as.factor(MImodel[,1])
MImodel[,2] = as.factor(MImodel[,2])
MImodel[,3] = as.factor(MImodel[,3])
MImodel[,4] = as.factor(MImodel[,4])
MImodel[,5] = as.factor(MImodel[,5])
MImodel[,6] = as.factor(MImodel[,6])
MImodel[,7] = as.numeric(MImodel[,7])
MImodel[,8] = as.numeric(MImodel[,8])
MImodel[,9] = as.factor(MImodel[,9])
MImodel[,10] = as.numeric(MImodel[,10])
MImodel[,11] = as.numeric(MImodel[,11])
MImodel[,12] = as.numeric(MImodel[,12])
MImodel[,13] = as.factor(MImodel[,13])
MImodel[,14] = as.factor(MImodel[,14])
MImodel[,15] = as.factor(MImodel[,15])
MImodel[,16] = as.factor(MImodel[,16])
MImodel[,17] = as.factor(MImodel[,17])
MImodel[,18] = as.factor(MImodel[,18])
MImodel[,19] = as.numeric(MImodel[,19])
MImodel[,20] = as.factor(MImodel[,20])
MImodel[,21] = as.numeric(MImodel[,21])
MImodel[,22] = as.numeric(MImodel[,22])m = 5
imp = mice(MImodel,m = m)##
## iter imp variable
## 1 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 1 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 2 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 3 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 4 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 1 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 2 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 3 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 4 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag
## 5 5 all_coping_talkfamily all_coping_talkMH all_coping_copingthought all_coping_thinking coping_sum coping_sum_3avg all_coping_any SIUrge Self_Efficacy coping_sum_3avg.lag all_coping_talkfamily.lag all_coping_talkMH.lag all_coping_copingthought.lag all_coping_thinking.lag coping_sum.lag all_coping_any.lag SIUrge.lag Self_Efficacy.lag## Warning: Number of logged events: 326k=22
qhat = matrix(NA, nrow = m,ncol = k)
u = array(NA,dim = c(k,k,m))
for (i in 1:m) {
data.impute = mice::complete(imp,action = i)}
all_coping_talkfamily.imp = as.factor(data.impute[,1])
all_coping_talkMH.imp = as.factor(data.impute[,2])
all_coping_copingthought.imp = as.factor(data.impute[,3])
all_coping_thinking.imp = as.factor(data.impute[,4])
all_coping_talkfriend.imp = as.factor(data.impute[,5])
all_coping_dis_rel_combined.imp = as.factor(data.impute[,6])
coping_sum.imp = data.impute[,7]
coping_sum_3avg.imp = data.impute[,8]
all_coping_any.imp = as.factor(data.impute[,9])
SIUrge.imp = data.impute[,10]
Self_Efficacy.imp = data.impute[,11]
pdat31.imp<-data.frame(all_coping_talkfamily.imp = all_coping_talkfamily.imp,
all_coping_talkMH.imp = all_coping_talkMH.imp,
all_coping_crisisline.imp = all_coping_crisisline.imp,
all_coping_copingthought.imp = all_coping_copingthought.imp,
all_coping_thinking.imp = all_coping_thinking.imp,
all_coping_talkfriend.imp = all_coping_talkfriend.imp,
all_coping_dis_rel_combined.imp = all_coping_dis_rel_combined.imp,
all_coping_any.imp = all_coping_any.imp,
SIUrge.imp = SIUrge.imp,
Self_Efficacy.imp = Self_Efficacy.imp,
coping_sum_3avg.imp = coping_sum_3avg.imp,
coping_sum.imp = coping_sum.imp)Restructuring Data file to create splines
na.df <- data.frame(SIUrge.imp = NA)
vars<-c("SIUrge.imp")
pdat31.1<-pdat31.imp[vars]
pdat31.2<- do.call(rbind, apply(pdat31.1, 1, function(x) {rbind(x, na.df)}))
na.df <- data.frame(all_coping_talkfamily.imp = NA,
all_coping_talkMH.imp = NA,
all_coping_copingthought.imp = NA,
all_coping_thinking.imp = NA,
all_coping_talkfriend.imp = NA,
all_coping_dis_rel_combined.imp = NA,
all_coping_any.imp = NA,
Self_Efficacy.imp = NA,
coping_sum.imp = NA,
coping_sum_3avg.imp = NA)
vars<-c("all_coping_talkfamily.imp",
"all_coping_talkMH.imp",
"all_coping_copingthought.imp",
"all_coping_thinking.imp",
"all_coping_talkfriend.imp",
"all_coping_dis_rel_combined.imp",
"all_coping_any.imp",
"Self_Efficacy.imp",
"coping_sum.imp",
"coping_sum_3avg.imp")
pdat31.3<-pdat31.imp[vars]
pdat31.4 <- do.call(rbind, apply(pdat31.3, 1, function(x) {rbind(na.df, x)}))
pdat31.imp<-cbind(pdat31.4, pdat31.2)
pdat31.imp$Day<-c(1:56)Creating splines
pdat31.imp<-data.frame(na.spline(pdat31.imp))
pdat31.imp<-round(pdat31.imp)
pdat31.imp$SIUrge.imp[pdat31.imp$SIUrge.imp>7]<-7
pdat31.imp$SIUrge.imp[pdat31.imp$SIUrge.imp<0]<-0
pdat31.imp$Self_Efficacy.imp[pdat31.imp$Self_Efficacy.imp>10]<-10
pdat31.imp$Self_Efficacy.imp[pdat31.imp$Self_Efficacy.imp<0]<-0Plotting SI urge over time by whether or not data was analyzed
vars<-c("Day", "SIUrge.imp")
pdat1.imp<-pdat1.imp[vars]
pdat1.imp$ID<-rep(201, times=56)
pdat2.imp<-pdat2.imp[vars]
pdat2.imp$ID<-rep(202, times=56)
pdat4.imp<-pdat4.imp[vars]
pdat4.imp$ID<-rep(204, times=56)
pdat5.imp<-pdat5.imp[vars]
pdat5.imp$Day<-c(1:56)
pdat5.imp$ID<-rep(205, times=56)
pdat6.imp<-pdat6.imp[vars]
pdat6.imp$ID<-rep(206, times=56)
pdat7.imp<-pdat7.imp[vars]
pdat7.imp$ID<-rep(207, times=56)
pdat8.imp<-pdat8.imp[vars]
pdat8.imp$ID<-rep(209, times=56)
pdat10.imp<-pdat10.imp[vars]
pdat10.imp$ID<-rep(211, times=56)
pdat11.imp<-pdat11.imp[vars]
pdat11.imp$ID<-rep(212, times=56)
pdat13.imp<-pdat13.imp[vars]
pdat13.imp$ID<-rep(214, times=56)
pdat18.imp<-pdat18.imp[vars]
pdat18.imp$ID<-rep(220, times=56)
pdat20.imp<-pdat20.imp[vars]
pdat20.imp$ID<-rep(222, times=56)
pdat21.imp<-pdat21.imp[vars]
pdat21.imp$ID<-rep(223, times=56)
pdat23.imp<-pdat23.imp[vars]
pdat23.imp$ID<-rep(225, times=56)
pdat24.imp<-pdat24.imp[vars]
pdat24.imp$ID<-rep(226, times=56)
pdat27.imp<-pdat27.imp[vars]
pdat27.imp$ID<-rep(229, times=56)
pdat28.imp<-pdat28.imp[vars]
pdat28.imp$ID<-rep(230, times=56)
pdat31.imp<-pdat31.imp[vars]
pdat31.imp$ID<-rep(233, times=56)
pdat34.imp<-pdat34.imp[vars]
pdat34.imp$ID<-rep(236, times=56)
data=rbind(pdat1.imp,pdat2.imp,pdat4.imp,pdat5.imp,pdat6.imp,pdat7.imp,pdat8.imp,pdat10.imp,pdat11.imp,pdat13.imp,pdat18.imp,pdat20.imp,pdat21.imp,pdat23.imp,pdat24.imp,pdat27.imp,pdat28.imp,pdat31.imp,pdat34.imp)
data_bg=data.frame("ID" = unique(data$ID), "group"=c(0,1,1,1,0,0,1,0,1,1,0,0,0,1,0,1,1,0,1))
ID_names <- c(
'201'="XX1",
'202'="001",
'204'="002",
'205'="003",
'206'="XX2",
'207'="XX3",
'209'="004",
'211'="XX4",
'212'="005",
'214'="006",
'220'="XX5",
'222'="XX6",
'223'="007",
'225'="008",
'226'="XX7",
'229'="009",
'230'="010",
'233'="XX8",
'236'="011"
)
zp <- ggplot(data, aes(x = Day, y = SIUrge.imp)) + geom_line(data = data, aes(x = Day, y = SIUrge.imp, group = ID), alpha = 1/2, size = 1/2) + geom_line(size = 1) + facet_wrap(~ID, labeller=labeller(ID=ID_names)) + ylim(0,8) + labs (y = "Suicidal Urge", x = "Day of Study") + theme_bw() + geom_rect(data=data_bg, aes(fill = as.factor(group)), inherit.aes = F, xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, alpha = 0.5) + scale_fill_grey(name = "SI Group", labels = c("< 5 obs", "> 5 obs"))
table(data$SIUrge.imp>0, data$ID)##
## 201 202 204 205 206 207 209 211 212 214 220 222 223 225 226 229 230 233
## FALSE 47 4 43 21 49 48 36 48 2 2 49 42 40 25 48 43 32 47
## TRUE 9 52 13 35 7 8 20 8 54 54 7 14 16 31 8 13 24 9
##
## 236
## FALSE 1
## TRUE 55jpeg("SI group.jpeg", res=300, height=6, width=9, units="in")
zp
dev.off()## quartz_off_screen
## 2