Convenience function for fitting community occupancy models (defined in a commOccu object) in JAGS or Nimble.
# S4 method for commOccu
fit(
object,
n.iter = 100,
thin = 1,
n.burnin = 0,
n.adapt = 0,
cores = 1,
chains = 3,
compile = TRUE,
WAIC = FALSE,
quiet = FALSE,
...
)commOccu object
number of iterations to monitor
thinning interval for monitors
burnin length
Length of adaptive phase
number of cores to utilize
number of MCMC chains to run
logical. If Nimble model, compile model with compileNimble before running model?
logical. Return WAIC (only Nimble models)
if TRUE messages and progress bar will be suppressed
additional arguments to pass to runMCMC (only relevant for Nimble)
A coda::mcmc.list
Models will be fit either in JAGS or Nimble, depending on the decision made in the nimble argument in communityModel.
For Nimble, compilation is strongly recommended for long model runs. Uncompiled models can run extremely slow. Compilation itself can take a while also, and requires that Rtools is available on the system.
It is a convenience function only which hides some of the configuration options. If you require more control over model fitting, you can run all steps individually. See vignette 5 for details.