predict-commOccu-method: Spatial predictions from community occupancy models

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

Spatial predictions from community occupancy models

Description

Create spatial predictions of species occupancy and species richness from community occupancy models and raster stacks.

Usage

## S4 method for signature 'commOccu'
predict(
  object,
  mcmc.list,
  type,
  draws = 1000,
  level = 0.95,
  interval = c("none", "confidence"),
  x,
  speciesSubset
)

Arguments

object	commOccu object
mcmc.list	mcmc.list. Output of fit called on a commOccu object
type	character. "psi" for species occupancy estimates, "richness" for species richness estimates
draws	Number of draws from the posterior to use when generating the plots. If fewer than draws are available, they are all used
level	Probability mass to include in the uncertainty interval
interval	# Type of interval calculation. Can be "none" or "confidence". Can be slow for type = "psi" with many cells and posterior samples. Can be abbreviated.
x	raster stack or data.frame. Must be scaled with same parameters as site covariates used in model, and have same names.
speciesSubset	species to include in richness estimates. Can be index number or species names.

Value

A raster stack or data.frame, depending on x

camtrapR documentation built on May 11, 2022, 5:18 p.m.