Simple bivariate ctsem

bivarate.R

# The current manual is here:
# https://cran.r-project.org/web/packages/ctsem/vignettes/hierarchicalmanual.pdf
# A few blog posts with examples are here: https://cdriver.netlify.app/

# Here's a bivariate panel example script:

library(ctsem)
data(AnomAuth)
longdat <- ctDeintervalise(ctWideToLong(AnomAuth,Tpoints = 5,n.manifest = 2))

sm<-ctModel(type='stanct',id='id',time = 'time',
  manifestNames = c('Y1','Y2'),
  MANIFESTVAR=0, #disables measurement error for this example
  LAMBDA=matrix(c(1, 0, 0, 1), nrow=2, ncol=2))

ctModelLatex(sm)

#default is to allow 'trait' type effects -- individual variation in intercept parameters. One way to disable is:
sm$pars$indvarying<- FALSE

sf=ctStanFit(longdat, ctstanmodel = sm,cores=6)

s=summary(sf)
print(s)

ctKalman(sf,plot=TRUE,kalmanvec=c('y','ysmooth'),subjects = c(1,3))
ctStanDiscretePars(sf,plot=TRUE)