predict-commOccu-method: Predictions from community occupancy models

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

Predictions from community occupancy models

Description

Create (spatial) predictions of species occupancy and species richness from community occupancy models and spatial rasters or covariate data frames.

Usage

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

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, "pao" for percentage of area occupied (by species), "psi_array" for raw occupancy probabilities in an array. For Royle-Nichols models, "abundance" for species abundance, or "lambda_array" for raw species abundance estimates in an array.
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 abbreviated). Calculation can be slow for type = "psi" with many cells and posterior samples.
x	SpatRaster or data.frame. Must be scaled with same parameters as site covariates used in model, and have same names.
aoi	SpatRaster with same dimensions as x (if x is a SpatRaster), indicating the area of interest (all cells with values are AOI, all NA cells are ignored). If NULL, predictions are made for all cells.
speciesSubset	species to include in richness estimates. Can be index number or species names.
batch	logical or numeric. If FALSE, all raster cells / data frame rows will be processed at once (can be memory intensive). If TRUE, computation is conducted in batches of 1000. If numeric, it is the desired batch size.
seed	numeric. Seed to use in set.seed for reproducible results (ensures that draws are identical).

Details

Processing can be very memory-intensive. If memory is insufficient, use the batch parameter. This can enable processing for higher numbers of draws or very large rasters / data frames.

Value

A SpatRaster or data.frame, depending on x. If type = "pao", a list. If type = "psi_array" or "lambda_array", a 3D-array [cell, species, draw].

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