# Single-Species, Multi-Species, and Integrated Spatial Occupancy Models

## Documentation for package ‘spOccupancy’ version 0.3.1

- DESCRIPTION file.

## Help Pages

fitted.intPGOcc | Extract Model Fitted Values for intPGOcc Object
fitted.lfJSDM | Extract Model Fitted Values for lfJSDM Object
fitted.lfMsPGOcc | Extract Model Fitted Values for lfMsPGOcc Object
fitted.msPGOcc | Extract Model Fitted Values for msPGOcc Object
fitted.PGOcc | Extract Model Fitted Values for PGOcc Object
fitted.sfJSDM | Extract Model Fitted Values for sfJSDM Object
fitted.sfMsPGOcc | Extract Model Fitted Values for sfMsPGOcc Object
fitted.spIntPGOcc | Extract Model Fitted Values for spIntPGOcc Object
fitted.spMsPGOcc | Extract Model Fitted Values for spMsPGOcc Object
fitted.spPGOcc | Extract Model Fitted Values for spPGOcc Object
hbef2015 | Detection-nondetection data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest
hbefElev | Elevation in meters extracted at a 30m resolution across the Hubbard Brook Experimental Forest
intPGOcc | Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables
lfJSDM | Function for Fitting a Latent Factor Joint Species Distribution Model
lfMsPGOcc | Function for Fitting Latent Factor Multi-Species Occupancy Models
msPGOcc | Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables
neon2015 | Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA
PGOcc | Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables
ppcOcc | Function for performing posterior predictive checks
predict.intPGOcc | Function for prediction at new locations for single-species integrated occupancy models
predict.lfJSDM | Function for prediction at new locations for latent factor joint species distribution models
predict.lfMsPGOcc | Function for prediction at new locations for latent factor multi-species occupancy models
predict.msPGOcc | Function for prediction at new locations for multi-species occupancy models
predict.PGOcc | Function for prediction at new locations for single-species occupancy models
predict.sfJSDM | Function for prediction at new locations for spatial factor joint species distribution model
predict.sfMsPGOcc | Function for prediction at new locations for spatial factor multi-species occupancy models
predict.spIntPGOcc | Function for prediction at new locations for single-species integrated spatial occupancy models
predict.spMsPGOcc | Function for prediction at new locations for multi-species spatial occupancy models
predict.spPGOcc | Function for prediction at new locations for single-species spatial occupancy models
print.intPGOcc | Methods for intPGOcc Object
print.lfJSDM | Methods for lfJSDM Object
print.lfMsPGOcc | Methods for lfMsPGOcc Object
print.msPGOcc | Methods for msPGOcc Object
print.PGOcc | Methods for PGOcc Object
print.sfJSDM | Methods for sfJSDM Object
print.sfMsPGOcc | Methods for sfMsPGOcc Object
print.spIntPGOcc | Methods for spIntPGOcc Object
print.spMsPGOcc | Methods for spMsPGOcc Object
print.spPGOcc | Methods for spPGOcc Object
sfJSDM | Function for Fitting a Spatial Factor Joint Species Distribution Model
sfMsPGOcc | Function for Fitting Spatial Factor Multi-Species Occupancy Models
simIntOcc | Simulate Single-Species Detection-Nondetection Data from Multiple Data Sources
simMsOcc | Simulate Multi-Species Detection-Nondetection Data
simOcc | Simulate Single-Species Detection-Nondetection Data
spIntPGOcc | Function for Fitting Single-Species Integrated Spatial Occupancy Models Using Polya-Gamma Latent Variables
spMsPGOcc | Function for Fitting Multi-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
spPGOcc | Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
summary.intPGOcc | Methods for intPGOcc Object
summary.lfJSDM | Methods for lfJSDM Object
summary.lfMsPGOcc | Methods for lfMsPGOcc Object
summary.msPGOcc | Methods for msPGOcc Object
summary.PGOcc | Methods for PGOcc Object
summary.ppcOcc | Methods for ppcOcc Object
summary.sfJSDM | Methods for sfJSDM Object
summary.sfMsPGOcc | Methods for sfMsPGOcc Object
summary.spIntPGOcc | Methods for spIntPGOcc Object
summary.spMsPGOcc | Methods for spMsPGOcc Object
summary.spPGOcc | Methods for spPGOcc Object
waicOcc | Compute Widely Applicable Information Criterion for spOccupancy Model Objects