Created
August 23, 2014 12:54
Recovering correlations
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
### R code from vignette source 'recoveringcorrelations.Rnw' | |
################################################### | |
### code chunk number 1: recoveringcorrelations.Rnw:93-151 | |
################################################### | |
new.df <- function(cond1.rt=487, effect.size=123, | |
sdev=544, | |
sdev.int.subj=160, sdev.slp.subj=195, | |
rho.u=0.6, | |
nsubj=37, | |
sdev.int.items=154, sdev.slp.items=142, | |
rho.w=0.6, | |
nitems=15) { | |
library(MASS) | |
ncond <- 2 | |
subj <- rep(1:nsubj, each=nitems*ncond) | |
item <- rep(1:nitems, nsubj, each=ncond) | |
cond <- rep(0:1, nsubj*nitems) | |
err <- rnorm(nsubj*nitems*ncond, 0, sdev) | |
d <- data.frame(subj=subj, item=item, | |
cond=cond+1, err=err) | |
Sigma.u<-matrix(c(sdev.int.subj^2, | |
rho.u*sdev.int.subj*sdev.slp.subj, | |
rho.u*sdev.int.subj*sdev.slp.subj, | |
sdev.slp.subj^2),nrow=2) | |
Sigma.w<-matrix(c(sdev.int.items^2, | |
rho.u*sdev.int.items*sdev.slp.items, | |
rho.u*sdev.int.items*sdev.slp.items, | |
sdev.slp.items^2),nrow=2) | |
# Adding random intercepts and slopes for subjects: | |
## first col. has adjustment for intercept, | |
## secdon col. has adjustment for slope | |
subj.rand.effs<-mvrnorm(n=nsubj,rep(0,ncond),Sigma.u) | |
item.rand.effs<-mvrnorm(n=nitems,rep(0,ncond),Sigma.w) | |
re.int.subj <- subj.rand.effs[,1] | |
d$re.int.subj <- rep(re.int.subj, each=nitems*ncond) | |
re.slp.subj <- subj.rand.effs[,2] | |
d$re.slp.subj <- rep(re.slp.subj, | |
each=nitems*ncond) * (cond - 0.5) | |
re.int.item <- item.rand.effs[,1] | |
d$re.int.item <- rep(re.int.item, nsubj, each=ncond) | |
re.slp.item <- item.rand.effs[,2] | |
d$re.slp.item <- rep(re.slp.item, nsubj, | |
each=ncond) * (cond - 0.5) | |
d$rt <- (cond1.rt + cond*effect.size | |
+ d$re.int.subj + d$re.slp.subj | |
+ d$re.int.item + d$re.slp.item | |
+ d$err) | |
return(list(d,cor(re.int.subj,re.slp.subj), | |
cor(re.int.item,re.slp.item))) | |
} | |
################################################### | |
### code chunk number 2: recoveringcorrelations.Rnw:156-165 | |
################################################### | |
gendata<-function(subjects=37,items=15){ | |
dat<-new.df(nsubj=subjects,nitems=items, | |
rho.u=0.6,rho.w=0.6) | |
dat <- dat[[1]] | |
dat<-dat[,c(1,2,3,9)] | |
dat$x<-ifelse(dat$cond==1,-0.5,0.5) | |
return(dat) | |
} | |
################################################### | |
### code chunk number 3: recoveringcorrelations.Rnw:170-171 | |
################################################### | |
nsim<-100 | |
################################################### | |
### code chunk number 4: recoveringcorrelations.Rnw:179-190 | |
################################################### | |
library(lme4) | |
subjcorr<-rep(NA,nsim) | |
itemcorr<-rep(NA,nsim) | |
for(i in 1:nsim){ | |
#print(i) | |
dat<-gendata() | |
m3<-lmer(rt~x+(1+x|subj)+(1+x|item),dat) | |
subjcorr[i]<-attr(VarCorr(m3)$subj,"correlation")[1,2] | |
itemcorr[i]<-attr(VarCorr(m3)$item,"correlation")[1,2] | |
} | |
################################################### | |
### code chunk number 5: recoveringcorrelations.Rnw:193-200 | |
################################################### | |
op<-par(mfrow=c(1,2),pty="s") | |
hist(subjcorr,freq=FALSE,xlab=expression(hat(rho)[u]), | |
main="Distribution of subj. corr.") | |
abline(v=0.6,lwd=3) | |
hist(itemcorr,freq=FALSE,xlab=expression(hat(rho)[w]), | |
main="Distribution of item corr.") | |
abline(v=0.6,lwd=3) | |
################################################### | |
### code chunk number 6: recoveringcorrelations.Rnw:205-215 | |
################################################### | |
subjcorr<-rep(NA,nsim) | |
itemcorr<-rep(NA,nsim) | |
for(i in 1:nsim){ | |
#print(i) | |
dat<-gendata(subjects=50,items=30) | |
m3<-lmer(rt~x+(1+x|subj)+(1+x|item),dat) | |
subjcorr[i]<-attr(VarCorr(m3)$subj,"correlation")[1,2] | |
itemcorr[i]<-attr(VarCorr(m3)$item,"correlation")[1,2] | |
} | |
################################################### | |
### code chunk number 7: recoveringcorrelations.Rnw:218-225 | |
################################################### | |
op<-par(mfrow=c(1,2),pty="s") | |
hist(subjcorr,freq=FALSE,xlab=expression(hat(rho)[u]), | |
main="Distribution of subj. corr.") | |
abline(v=0.6,lwd=3) | |
hist(itemcorr,freq=FALSE,xlab=expression(hat(rho)[w]), | |
main="Distribution of item corr.") | |
abline(v=0.6,lwd=3) | |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment