fit,commOccu-method {camtrapR}

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 signature '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,
  ...
)

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.

Value

A coda::mcmc.list