Nothing
if(identical(Sys.getenv("NOT_CRAN"), "true")& .Machine$sizeof.pointer != 4){
library(ctsem)
library(testthat)
cores = 2
context('misc')
test_that("loo", {
# for(cores in c(1,cores)){
#cores=6
data(AnomAuth)
AnomAuthmodel<-ctModel(LAMBDA=matrix(c(1, 0, 0, 1), nrow=2, ncol=2),
n.latent=2,n.manifest=2,
# TIpredNames = 'Y1',
# DRIFT=c('dr1||||Y1','dr12||||Y1','dr21||||Y1','dr22||||Y1'),
MANIFESTVAR=diag(0,2),
Tpoints=5)
aa=ctDeintervalise(ctWideToLong(AnomAuth[1:500,],
Tpoints = AnomAuthmodel$Tpoints,n.manifest = 2))
aa[4:20,AnomAuthmodel$manifestNames] <- NA
sm <- ctStanModel(AnomAuthmodel,tipredDefault = FALSE)
sm$pars$indvarying<- FALSE
sf=ctStanFit(aa,
ctstanmodel = sm, optimize=TRUE,verbose=0,savescores = FALSE,cores=cores)
sdat <- sf$standata
sdat$dokalmanrows[sdat$subject==1] <- 0L #remove 1 subject
smf <- stan_reinitsf(sf$stanmodel,sdat)
test_isclose(
sf$stanfit$optimfit$value - rstan::log_prob(smf,sf$stanfit$rawest), #check ll equiv
sum(sf$stanfit$transformedparsfull$llrow[sdat$subject==1]))
loo=ctLOO(fit = sf,folds = 10,cores=cores,parallelFolds = T,subjectwise = T)
loo2=ctLOO(fit = sf,folds = 10,cores=cores,parallelFolds = F,subjectwise = T)
test_isclose(
mean(loo2$outsampleLogLikRow-loo$outsampleLogLikRow),
0,tol=.01)
test_isclose(
sum(loo$insampleLogLikRow),
sum(sf$stanfit$transformedparsfull$llrow),tol=.1)
test_isclose(
sum(loo2$insampleLogLikRow),
sum(sf$stanfit$transformedparsfull$llrow),tol=.1)
})
}
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