fit,commOccu-method: Fit a community (multi-species) occupancy model

Description

Convenience function for fitting community occupancy models (defined in a commOccu object) in JAGS or Nimble.

Usage

# S4 method for commOccu
fit(
  object,
  n.iter = 100,
  thin = 1,
  n.burnin = n.iter/2,
  n.adapt = 0,
  chains = 3,
  inits = NULL,
  compile = TRUE,
  WAIC = FALSE,
  quiet = FALSE,
  ...
)

Value

A coda::mcmc.list

Arguments

object: commOccu object
n.iter: number of iterations to monitor
thin: thinning interval for monitors
n.burnin: burnin length. Defaults to half of n.iter.
n.adapt: Length of adaptive phase
chains: number of MCMC chains to run
inits: named list. Initial values to use. If NULL (default), the values from the inits function in object are used.
compile: logical. If Nimble model, compile model with compileNimble before running model?
WAIC: logical. Return WAIC (only Nimble models)
quiet: if TRUE messages and progress bar will be suppressed
...: additional arguments to pass to runMCMC (only relevant for Nimble)

Details

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.

This 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.