R2Star Clinical Models

Load Packages

library(mgcv)
library(voxel)
library('knitr')
library(visreg)

Read in r2star data

r2star <- read.csv("r2star_finalSample_03152017.csv")

Set age and sex variables

r2star$sex <- ordered(r2star$sex)
sex <- r2star$sex
age <- (r2star$ageAtScan1)/12

Set striatal regions

rpallidum <- r2star$Right.Pallidum
lpallidum <- r2star$Left.Pallidum
pallidum <- (r2star$Right.Pallidum + r2star$Left.Pallidum)/2

raccumbems <- r2star$Right.Accumbens.Area
laccumbens <- r2star$Left.Accumbens.Area
accumbens <- (r2star$Right.Accumbens.Area + r2star$Left.Accumbens.Area)/2

rcaudate <- r2star$Right.Caudate
lcaudate <- r2star$Left.Caudate
caudate <- (r2star$Right.Caudate + r2star$Left.Caudate)/2

rputamen <- r2star$Right.Putamen
lputamen <- r2star$Left.Putamen
putamen <- (r2star$Right.Putamen + r2star$Left.Putamen)/2

Set clinical variables

psychopath <- r2star$overall_psychopathology_4factorv2
psychosisCorr <- r2star$psychosis_corrtraitsv2

Striatal Models

Pallidum

pallidumPsych <- gam(pallidum ~ s(age) + sex + psychopath, data=r2star, method="REML")
visreg(pallidumPsych,"psychopath")

pall_psych_pval <- as.data.frame(summary(pallidumPsych)$p.table[3,4])
names(pall_psych_pval) <- "pallidum_psych_pval"
print(pall_psych_pval)

##   pallidum_psych_pval
## 1            0.457685

pallidumPsychosis <- gam(pallidum ~ s(age) + sex + psychosisCorr, data=r2star, method="REML")
visreg(pallidumPsychosis,"psychosisCorr")

pall_psychosis_pval <- as.data.frame(summary(pallidumPsychosis)$p.table[3,4])
names(pall_psychosis_pval) <- "pallidum_psychosis_pval"
print(pall_psychosis_pval)

##   pallidum_psychosis_pval
## 1               0.3770079

Accumbens

accumbensPsych <- gam(accumbens ~ s(age) + sex + psychopath, data=r2star, method="REML")
visreg(accumbensPsych,"psychopath")

acc_psych_pval <- as.data.frame(summary(accumbensPsych)$p.table[3,4])
names(acc_psych_pval) <- "accumbens_psych_pval"
print(acc_psych_pval)

##   accumbens_psych_pval
## 1            0.1803861

accumbensPsychosis <- gam(accumbens ~ s(age) + sex + psychosisCorr, data=r2star, method="REML")
visreg(accumbensPsychosis,"psychosisCorr")

acc_psychosis_pval <- as.data.frame(summary(accumbensPsychosis)$p.table[3,4])
names(acc_psychosis_pval) <- "accumbens_psychosis_pval"
print(acc_psychosis_pval)

##   accumbens_psychosis_pval
## 1                0.1458206

Caudate

caudatePsych <- gam(caudate ~ s(age) + sex + psychopath, data=r2star, method="REML")
visreg(caudatePsych,"psychopath")

cau_psych_pval <- as.data.frame(summary(caudatePsych)$p.table[3,4])
names(cau_psych_pval) <- "caudate_psych_pval"
print(cau_psych_pval)

##   caudate_psych_pval
## 1          0.8584872

caudatePsychosis <- gam(caudate ~ s(age) + sex + psychosisCorr, data=r2star, method="REML")
visreg(caudatePsychosis,"psychosisCorr")

cau_psychosis_pval <- as.data.frame(summary(caudatePsychosis)$p.table[3,4])
names(cau_psychosis_pval) <- "caudate_psychosis_pval"
print(cau_psychosis_pval)

##   caudate_psychosis_pval
## 1              0.6531786

Putamen

putamenPsych <- gam(putamen ~ s(age) + sex + psychopath, data=r2star, method="REML")
visreg(putamenPsych,"psychopath")

put_psych_pval <- as.data.frame(summary(putamenPsych)$p.table[3,4])
names(put_psych_pval) <- "putamen_psych_pval"
print(put_psych_pval)

##   putamen_psych_pval
## 1        0.001122039

putamenPsychosis <- gam(putamen ~ s(age) + sex + psychosisCorr, data=r2star, method="REML")
visreg(putamenPsychosis,"psychosisCorr")

put_psychosis_pval <- as.data.frame(summary(putamenPsychosis)$p.table[3,4])
names(put_psychosis_pval) <- "putamen_psychosis_pval"
print(put_psychosis_pval)

##   putamen_psychosis_pval
## 1           0.0008787197

P values

pvalues = list(pall_psych_pval, pall_psychosis_pval, acc_psych_pval, acc_psychosis_pval, cau_psych_pval, cau_psychosis_pval, put_psych_pval, put_psychosis_pval)
pvals <- Reduce(merge, lapply(pvalues, function(x) data.frame(x, rn = row.names(x))))
print(pvals)

##   rn pallidum_psych_pval pallidum_psychosis_pval accumbens_psych_pval
## 1  1            0.457685               0.3770079            0.1803861
##   accumbens_psychosis_pval caudate_psych_pval caudate_psychosis_pval
## 1                0.1458206          0.8584872              0.6531786
##   putamen_psych_pval putamen_psychosis_pval
## 1        0.001122039           0.0008787197