Nothing
if(identical(Sys.getenv("NOT_CRAN"), "true")& .Machine$sizeof.pointer != 4){
library(ctsem)
library(testthat)
set.seed(2)
context("tipredcheck")
test_that("simpleTIpredcheck", {
Tpoints=10
n.manifest=1
n.TDpred=0
n.TIpred=1
n.latent=1
n.subjects=50
TI1 <- rnorm(n.subjects)
gm<-ctModel(type='omx', Tpoints=Tpoints,n.latent=n.latent,
n.TDpred=n.TDpred,n.manifest=n.manifest,
MANIFESTVAR=diag(0.5,1),
LAMBDA=diag(1,1),T0MEANS=100,
DRIFT=matrix(c(-.3),nrow=1),
DIFFUSION=matrix(c(2),1),
T0VAR=diag(10,1))
for(i in 1:n.subjects){
gm$CINT[1,1] <- TI1[i]*5+rnorm(1,0,.6)
ndat<-suppressMessages(ctGenerate(gm,n.subjects=1,burnin=10,logdtsd=.4))
ndat <- cbind(ndat,TI1[i])
ndat[,1] <- i
if(i>1) tdat <- rbind(tdat,ndat) else tdat <- ndat
}
colnames(tdat)[4] <- 'TI1'
tdat[2,'Y1'] <- NA
tdat[tdat[,'id']==2,'TI1'] <- NA
checkm<-suppressMessages(ctModel(type='stanct',Tpoints=Tpoints,
MANIFESTVAR=diag(0.5,1),
DRIFT=matrix(c(-.3),nrow=1),
DIFFUSION=matrix(c(2),1),
n.latent=n.latent,n.TDpred=n.TDpred,
n.TIpred=n.TIpred,
MANIFESTMEANS=matrix(0,nrow=n.manifest),
CINT=matrix(c('cint1'),ncol=1),
n.manifest=n.manifest,LAMBDA=diag(1)))
# checkm$pars$indvarying <- FALSE
checkm$pars[c(-1,-7) ,c('TI1_effect')] <- FALSE
tfit1<-ctStanFit(tdat,checkm,chains=1,cores=2,optimize=TRUE,
optimcontrol=list(is=TRUE,finishsamples=500),
priors=TRUE,verbose=0)
s1=summary(tfit1)
expect_equivalent(s1$tipreds[2,'mean'],5,tolerance=.1)
expect_equivalent(s1$popsd[2,'mean'],.6,tolerance=.2)
tfit2<-ctStanFit(tdat,checkm,optimize=TRUE,cores=2,verbose=0,
optimcontrol=list(is=FALSE),priors=TRUE)
s2=summary(tfit2)
expect_equivalent(s2$tipreds[2,'mean'],5,tolerance=.1)
expect_equivalent(s2$popsd[2,'mean'],.6,tolerance=.2)
tfit3<-suppressWarnings(ctStanFit(tdat,checkm,iter=300,chains=2,optimize=FALSE,
control=list(adapt_delta=.8,max_treedepth=6),plot=FALSE))
s3=summary(tfit3)
expect_equivalent(s3$tipreds[2,'mean'],5,tolerance=.1)
expect_equivalent(s3$popsd[2,'mean'],.6,tolerance=.2)
})
}
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