data-raw/pied-flycatchers-1-mcmc.R

In sjbonner/dalmatian: Automating the Fitting of Double Linear Mixed Models in 'JAGS' and 'nimble'

## Load packages
library(devtools)

## Load dalmatian
devtools::load_all()

## Load pied flycatcher data
data(pied_flycatchers_1)


## Create variables bounding the true load
pfdata$lower=ifelse(pfdata$load==0,log(.001),log(pfdata$load-.049))
pfdata$upper=log(pfdata$load+.05)

##### Model 1 #####

## Mean model
mymean=list(fixed=list(name="alpha",
       formula=~ log(IVI) + broodsize + sex,
       priors=list(c("dnorm",0,.001))))

## Dispersion model
mydisp=list(fixed=list(name="psi",
                       formula=~broodsize + sex,
                       priors=list(c("dnorm",0,.001))),
            link="log")

## Set working directory
workingDir <- tempdir()

## Define list of arguments for jags.model()
jm.args <- list(file=file.path(workingDir,"pied_flycatcher_1_jags.R"),n.adapt=1000)

## Define list of arguments for coda.samples()
cs.args <- list(n.iter=5000,thin=20)

## Run the model using dalmatian
pfmcmc <- dalmatian(df=pfdata,
                       mean.model=mymean,
                       dispersion.model=mydisp,
                       jags.model.args=jm.args,
                       coda.samples.args=cs.args,
                       rounding=TRUE,
                       lower="lower",
                       upper="upper",
                       n.cores = 3,
                       residuals = FALSE,
                       overwrite = TRUE,
                       debug=FALSE)

file <- file.path(proj_path(),"data-mcmc","pfmcmc1.RData")
save(pfmcmc1, file = file)