library(mice)
library(haven)
dr <- read_sav("H:/ALG Statistics and Methodology/Analyses/Rafael Gomide/June 29 2018/Ms#2intraarch, prepared for analysis.sav")
View(dr)
dr<-dr[,-2]
dr<-dr[,-c(42:47)]



ptm<-proc.time()
Increm_AAL_U<-NA
Increm_TAL_U<-NA
Increm_P_U<-NA
Increm_AAL_L<-NA
Increm_TAL_L<-NA
Increm_P_L<-NA
IOTNneed_YN<-NA
DEspaceoverallmean<-NA

dr_new<-cbind(dr,Increm_AAL_U,Increm_TAL_U,Increm_P_U,Increm_AAL_L,Increm_TAL_L,Increm_P_L,IOTNneed_YN,DEspaceoverallmean)
dr.ini<-mice(dr,m=1,seed=1000)

meth <- dr.ini$meth
#set new to passive imputation 
meth["Increm_AAL_U"] <- "~ I(AAL_U_4-AAL_U_1)"
meth["Increm_TAL_U"] <- "~ I(TAL_U_4-TAL_U_1)"
meth["Increm_P_U"] <- "~ I(P_U_4-P_U_1)"
meth["Increm_AAL_L"] <- "~ I(AAL_L_4-AAL_L_1)"
meth["Increm_TAL_L"] <- "~ I(TAL_L_4-TAL_L_1)"
meth["Increm_P_L"] <- "~ I(P_L_4-P_L_1)"
meth["IOTNneed_YN"] <- "~ I(IOTN>2)"
meth["DEspaceoverallmean"] <- "~ I((SpaceDE_L_1_mean+SpaceDE_U_1_mean+SpaceDE_L_4_mean+SpaceDE_U_4_mean)/2)"  #Do divide by 4 as opposed to 2
dr.100 <- mice(dr_new, meth=meth,m=100)
diff<-proc.time()-ptm
diff


anal_aal_u.0.a<-with(dr.100,lm(AAL_U_1~Age+Gender+ART+UCT+SpaceDE_U_1_mean))
overall_anal_aal_u.0.a<-summary(pool(anal_aal_u.0.a))
anal_tal_u.0.a<-with(dr.100,lm(TAL_U_1~Age+Gender+ART+UCT+SpaceDE_U_1_mean))
overall_anal_tal_u.0.a<-summary(pool(anal_tal_u.0.a))
anal_p_u.0.a<-with(dr.100,lm(P_U_1~Age+Gender+ART+UCT+SpaceDE_U_1_mean))
overall_anal_p_u.0.a<-summary(pool(anal_p_u.0.a))

anal_aal_l.0.a<-with(dr.100,lm(AAL_L_1~Age+Gender+ART+UCT+SpaceDE_L_1_mean))
overall_anal_aal_l.0.a<-summary(pool(anal_aal_l.0.a))
anal_tal_l.0.a<-with(dr.100,lm(TAL_L_1~Age+Gender+ART+UCT+SpaceDE_L_1_mean))
overall_anal_tal_l.0.a<-summary(pool(anal_tal_l.0.a))
anal_p_l.0.a<-with(dr.100,lm(P_L_1~Age+Gender+ART+UCT+SpaceDE_L_1_mean))
overall_anal_p_l.0.a<-summary(pool(anal_p_l.0.a))




anal_aal_u.4.a<-with(dr.100,lm(AAL_U_4~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_aal_u.4.a<-summary(pool(anal_aal_u.4.a))
anal_tal_u.4.a<-with(dr.100,lm(TAL_U_4~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_tal_u.4.a<-summary(pool(anal_tal_u.4.a))
anal_p_u.4.a<-with(dr.100,lm(P_U_4~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_p_u.4.a<-summary(pool(anal_p_u.4.a))

anal_aal_l.4.a<-with(dr.100,lm(AAL_L_4~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_aal_l.4.a<-summary(pool(anal_aal_l.4.a))
anal_tal_l.4.a<-with(dr.100,lm(TAL_L_4~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_tal_l.4.a<-summary(pool(anal_tal_l.4.a))
anal_p_l.4.a<-with(dr.100,lm(P_L_4~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_p_l.4.a<-summary(pool(anal_p_l.4.a))


anal_aal_u.incr.a<-with(dr.100,lm(Increm_AAL_U~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_aal_u.incr.a<-summary(pool(anal_aal_u.incr.a))
anal_tal_u.incr.a<-with(dr.100,lm(Increm_TAL_U~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_tal_u.incr.a<-summary(pool(anal_tal_u.incr.a))
anal_p_u.incr.a<-with(dr.100,lm(Increm_P_U~Age+Gender+ART+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_p_u.incr.a<-summary(pool(anal_p_u.incr.a))

anal_aal_l.incr.a<-with(dr.100,lm(Increm_AAL_U~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_aal_l.incr.a<-summary(pool(anal_aal_l.incr.a))
anal_tal_l.incr.a<-with(dr.100,lm(Increm_TAL_U~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_tal_l.incr.a<-summary(pool(anal_tal_l.incr.a))
anal_p_l.incr.a<-with(dr.100,lm(Increm_P_U~Age+Gender+ART+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_p_l.incr.a<-summary(pool(anal_p_l.incr.a))

anal_iotn_yn.a <- glm.mids(IOTNneed_YN~Age+Gender+ART+UCT+DEspaceoverallmean, data=dr.100, family = binomial)
overall_anal_iotn_yn.a<-summary(pool(anal_iotn_yn.a))

anal_aal_u.0.b<-with(dr.100,lm(AAL_U_1~Age+Gender+CRT+UCT+SpaceDE_U_1_mean))
overall_anal_aal_u.0.b<-summary(pool(anal_aal_u.0.b))
anal_tal_u.0.b<-with(dr.100,lm(TAL_U_1~Age+Gender+CRT+UCT+SpaceDE_U_1_mean))
overall_anal_tal_u.0.b<-summary(pool(anal_tal_u.0.b))
anal_p_u.0.b<-with(dr.100,lm(P_U_1~Age+Gender+CRT+UCT+SpaceDE_U_1_mean))
overall_anal_p_u.0.b<-summary(pool(anal_p_u.0.b))

anal_aal_l.0.b<-with(dr.100,lm(AAL_L_1~Age+Gender+CRT+UCT+SpaceDE_L_1_mean))
overall_anal_aal_l.0.b<-summary(pool(anal_aal_l.0.b))
anal_tal_l.0.b<-with(dr.100,lm(TAL_L_1~Age+Gender+CRT+UCT+SpaceDE_L_1_mean))
overall_anal_tal_l.0.b<-summary(pool(anal_tal_l.0.b))
anal_p_l.0.b<-with(dr.100,lm(P_L_1~Age+Gender+CRT+UCT+SpaceDE_L_1_mean))
overall_anal_p_l.0.b<-summary(pool(anal_p_l.0.b))




anal_aal_u.4.b<-with(dr.100,lm(AAL_U_4~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_aal_u.4.b<-summary(pool(anal_aal_u.4.b))
anal_tal_u.4.b<-with(dr.100,lm(TAL_U_4~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_tal_u.4.b<-summary(pool(anal_tal_u.4.b))
anal_p_u.4.b<-with(dr.100,lm(P_U_4~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_p_u.4.b<-summary(pool(anal_p_u.4.b))

anal_aal_l.4.b<-with(dr.100,lm(AAL_L_4~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_aal_l.4.b<-summary(pool(anal_aal_l.4.b))
anal_tal_l.4.b<-with(dr.100,lm(TAL_L_4~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_tal_l.4.b<-summary(pool(anal_tal_l.4.b))
anal_p_l.4.b<-with(dr.100,lm(P_L_4~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_p_l.4.b<-summary(pool(anal_p_l.4.b))


anal_aal_u.incr.b<-with(dr.100,lm(Increm_AAL_U~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_aal_u.incr.b<-summary(pool(anal_aal_u.incr.b))
anal_tal_u.incr.b<-with(dr.100,lm(Increm_TAL_U~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_tal_u.incr.b<-summary(pool(anal_tal_u.incr.b))
anal_p_u.incr.b<-with(dr.100,lm(Increm_P_U~Age+Gender+CRT+UCT+SpaceDE_U_1_mean+SpaceDE_U_4_mean))
overall_anal_p_u.incr.b<-summary(pool(anal_p_u.incr.b))

anal_aal_l.incr.b<-with(dr.100,lm(Increm_AAL_U~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_aal_l.incr.b<-summary(pool(anal_aal_l.incr.b))
anal_tal_l.incr.b<-with(dr.100,lm(Increm_TAL_U~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_tal_l.incr.b<-summary(pool(anal_tal_l.incr.b))
anal_p_l.incr.b<-with(dr.100,lm(Increm_P_U~Age+Gender+CRT+UCT+SpaceDE_L_1_mean+SpaceDE_L_4_mean))
overall_anal_p_l.incr.b<-summary(pool(anal_p_l.incr.b))

anal_iotn_yn.b <- glm.mids(IOTNneed_YN~Age+Gender+CRT+UCT+DEspaceoverallmean, data=dr.100, family = binomial)
overall_anal_iotn_yn.b<-summary(pool(anal_iotn_yn.b))



print("First CRT is reference for all analyses")
print("All output distances")
print("Baseline, first upper then lower")
print(overall_anal_aal_u.0.a)
print(overall_anal_tal_u.0.a)
print(overall_anal_p_u.0.a)
print(overall_anal_aal_l.0.a)
print(overall_anal_tal_l.0.a)
print(overall_anal_p_l.0.a)

print("T4, first upper then lower")
print(overall_anal_aal_u.4.a)
print(overall_anal_tal_u.4.a)
print(overall_anal_p_u.4.a)
print(overall_anal_aal_l.4.a)
print(overall_anal_tal_l.4.a)
print(overall_anal_p_l.4.a)

print("Increments, first upper then lower")
print(overall_anal_aal_u.incr.a)
print(overall_anal_tal_u.incr.a)
print(overall_anal_p_u.incr.a)
print(overall_anal_aal_l.incr.a)
print(overall_anal_tal_l.incr.a)
print(overall_anal_p_l.incr.a)

print("Analysis for IONT")
print(overall_anal_iotn_yn.a)


print("Now ART is reference for all analyses")
print("All output distances")
print("Baseline, first upper then lower")
print(overall_anal_aal_u.0.b)
print(overall_anal_tal_u.0.b)
print(overall_anal_p_u.0.b)
print(overall_anal_aal_l.0.b)
print(overall_anal_tal_l.0.b)
print(overall_anal_p_l.0.b)

print("T4, first upper then lower")
print(overall_anal_aal_u.4.b)
print(overall_anal_tal_u.4.b)
print(overall_anal_p_u.4.b)
print(overall_anal_aal_l.4.b)
print(overall_anal_tal_l.4.b)
print(overall_anal_p_l.4.b)

print("Increments, first upper then lower")
print(overall_anal_aal_u.incr.b)
print(overall_anal_tal_u.incr.b)
print(overall_anal_p_u.incr.b)
print(overall_anal_aal_l.incr.b)
print(overall_anal_tal_l.incr.b)
print(overall_anal_p_l.incr.b)

print("Analysis for IONT")
print(overall_anal_iotn_yn.b)




examp1<-with(dr.100,lm(AAL_U_1~Age+Gender+UCT+SpaceDE_U_1_mean))
overall_examp1<-summary(pool(examp1))
examp2<-with(dr.100,lm(AAL_U_1~Age+Gender+ART+CRT+SpaceDE_U_1_mean))
overall_examp2<-summary(pool(examp2))

print(overall_examp1)
print(overall_examp2)