fit,commOccu-method | R Documentation |
Convenience function for fitting community occupancy models (defined in a commOccu object) in JAGS or Nimble.
## S4 method for signature 'commOccu' fit( object, n.iter = 100, thin = 1, n.burnin = 0, n.adapt = 0, cores = 1, chains = 3, compile = TRUE, WAIC = FALSE, quiet = FALSE, ... )
object |
|
n.iter |
number of iterations to monitor |
thin |
thinning interval for monitors |
n.burnin |
burnin length |
n.adapt |
Length of adaptive phase |
cores |
number of cores to utilize |
chains |
number of MCMC chains to run |
compile |
logical. If Nimble model, compile model with |
WAIC |
logical. Return WAIC (only Nimble models) |
quiet |
if TRUE messages and progress bar will be suppressed |
... |
additional arguments to pass to |
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.
A coda::mcmc.list
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.