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

In camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

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

camtrapR documentation built on May 29, 2024, 6:45 a.m.