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

## Documentation for package ‘spOccupancy’ version 0.8.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

F G H I L M N P R S T U W

spOccupancy-package | Single-Species, Multi-Species, and Integrated Spatial Occupancy Models

## -- F --

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
fitted.stIntPGOcc | Extract Model Fitted Values for stIntPGOcc Object
fitted.stMsPGOcc | Extract Model Fitted Values for stMsPGOcc Object
fitted.stPGOcc | Extract Model Fitted Values for stPGOcc Object
fitted.svcMsPGOcc | Extract Model Fitted Values for svcMsPGOcc Object
fitted.svcPGBinom | Extract Model Fitted Values for svcPGBinom Object
fitted.svcPGOcc | Extract Model Fitted Values for svcPGOcc Object
fitted.svcTIntPGOcc | Extract Model Fitted Values for svcTIntPGOcc Object
fitted.svcTMsPGOcc | Extract Model Fitted Values for svcTMsPGOcc Object
fitted.svcTPGBinom | Extract Model Fitted Values for svcTPGBinom Object
fitted.svcTPGOcc | Extract Model Fitted Values for svcTPGOcc Object
fitted.tIntPGOcc | Extract Model Fitted Values for tIntPGOcc Object
fitted.tMsPGOcc | Extract Model Fitted Values for tMsPGOcc Object
fitted.tPGOcc | Extract Model Fitted Values for tPGOcc Object

## -- G --

getSVCSamples | Extract spatially-varying coefficient MCMC samples

## -- H --

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
hbefTrends | Detection-nondetection data of 12 foliage gleaning bird species from 2010-2018 in the Hubbard Brook Experimental Forest

## -- I --

intMsPGOcc | Function for Fitting Integrated Multi-Species Occupancy Models Using Polya-Gamma Latent Variables
intPGOcc | Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables

## -- L --

lfJSDM | Function for Fitting a Latent Factor Joint Species Distribution Model
lfMsPGOcc | Function for Fitting Latent Factor Multi-Species Occupancy Models

## -- M --

msPGOcc | Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables

## -- N --

neon2015 | Detection-nondetection data of 12 foliage gleaning bird species in 2015 in Bartlett Experimental Forest in New Hampshire, USA

## -- P --

PGOcc | Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables
plot.intMsPGOcc | Methods for intMsPGOcc Object
plot.intPGOcc | Methods for intPGOcc Object
plot.lfJSDM | Methods for lfJSDM Object
plot.lfMsPGOcc | Methods for lfMsPGOcc Object
plot.msPGOcc | Methods for msPGOcc Object
plot.PGOcc | Methods for PGOcc Object
plot.sfJSDM | Methods for sfJSDM Object
plot.sfMsPGOcc | Methods for sfMsPGOcc Object
plot.spIntPGOcc | Methods for spIntPGOcc Object
plot.spMsPGOcc | Methods for spMsPGOcc Object
plot.spPGOcc | Methods for spPGOcc Object
plot.stIntPGOcc | Methods for stIntPGOcc Object
plot.stMsPGOcc | Methods for stMsPGOcc Object
plot.stPGOcc | Methods for stPGOcc Object
plot.svcMsPGOcc | Methods for svcMsPGOcc Object
plot.svcPGBinom | Methods for svcPGBinom Object
plot.svcPGOcc | Methods for svcPGOcc Object
plot.svcTIntPGOcc | Methods for svcTIntPGOcc Object
plot.svcTMsPGOcc | Methods for svcTMsPGOcc Object
plot.svcTPGBinom | Methods for svcTPGBinom Object
plot.svcTPGOcc | Methods for svcTPGOcc Object
plot.tIntPGOcc | Methods for tIntPGOcc Object
plot.tMsPGOcc | Methods for tMsPGOcc Object
plot.tPGOcc | Methods for tPGOcc Object
postHocLM | Function for Fitting Linear Mixed Models with Previous Model Estimates
ppcOcc | Function for performing posterior predictive checks
predict.intMsPGOcc | Function for prediction at new locations for integrated multi-species occupancy models
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
predict.stIntPGOcc | Function for prediction at new locations for multi-season single-species spatial integrated occupancy models
predict.stMsPGOcc | Function for prediction at new locations for multi-season multi-species spatial occupancy models
predict.stPGOcc | Function for prediction at new locations for multi-season single-species spatial occupancy models
predict.svcMsPGOcc | Function for prediction at new locations for spatially varying coefficient multi-species occupancy models
predict.svcPGBinom | Function for prediction at new locations for single-species spatially-varying coefficient Binomial models
predict.svcPGOcc | Function for prediction at new locations for single-species spatially-varying coefficient occupancy models
predict.svcTIntPGOcc | Function for prediction at new locations for multi-season single-species spatially-varying coefficient integrated occupancy models
predict.svcTMsPGOcc | Function for prediction at new locations for multi-season multi-species spatially-varying coefficient occupancy models
predict.svcTPGBinom | Function for prediction at new locations for multi-season single-species spatially-varying coefficient binomial models
predict.svcTPGOcc | Function for prediction at new locations for multi-season single-species spatially-varying coefficient occupancy models
predict.tIntPGOcc | Function for prediction at new locations for multi-season single-species integrated occupancy models
predict.tMsPGOcc | Function for prediction at new locations for multi-season multi-species occupancy models
predict.tPGOcc | Function for prediction at new locations for multi-season single-species occupancy models
print.intMsPGOcc | Methods for intMsPGOcc Object
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.postHocLM | Methods for postHocLM 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
print.stIntPGOcc | Methods for stIntPGOcc Object
print.stMsPGOcc | Methods for stMsPGOcc Object
print.stPGOcc | Methods for stPGOcc Object
print.svcMsPGOcc | Methods for svcMsPGOcc Object
print.svcPGBinom | Methods for svcPGBinom Object
print.svcPGOcc | Methods for svcPGOcc Object
print.svcTIntPGOcc | Methods for svcTIntPGOcc Object
print.svcTMsPGOcc | Methods for svcTMsPGOcc Object
print.svcTPGBinom | Methods for svcTPGBinom Object
print.svcTPGOcc | Methods for svcTPGOcc Object
print.tIntPGOcc | Methods for tIntPGOcc Object
print.tMsPGOcc | Methods for tMsPGOcc Object
print.tPGOcc | Methods for tPGOcc Object

## -- R --

residuals.PGOcc | Occupancy and detection residuals for 'PGOcc' models
residuals.spPGOcc | Occupancy and detection residuals for 'spPGOcc' models
residuals.svcPGOcc | Occupancy and detection residuals for 'svcPGOcc' models

## -- S --

sfJSDM | Function for Fitting a Spatial Factor Joint Species Distribution Model
sfMsPGOcc | Function for Fitting Spatial Factor Multi-Species Occupancy Models
simBinom | Simulate Single-Species Binomial Data
simIntMsOcc | Simulate Multi-Species Detection-Nondetection Data from Multiple Data Sources
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
simTBinom | Simulate Multi-Season Single-Species Binomial Data
simTIntOcc | Simulate Single-Species Multi-Season Detection-Nondetection Data from Multiple Data Sources
simTMsOcc | Simulate Multi-Species Multi-Season Detection-Nondetection Data
simTOcc | Simulate Multi-Season 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
spOccupancy | Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
spPGOcc | Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
stIntPGOcc | Function for Fitting Multi-Season Single-Species Spatial Integrated Occupancy Models Using Polya-Gamma Latent Variables
stMsPGOcc | Function for Fitting Multi-Species Multi-Season Spatial Occupancy Models
stPGOcc | Function for Fitting Multi-Season Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables
summary.intMsPGOcc | Methods for intMsPGOcc Object
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.postHocLM | Methods for postHocLM 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
summary.stIntPGOcc | Methods for stIntPGOcc Object
summary.stMsPGOcc | Methods for stMsPGOcc Object
summary.stPGOcc | Methods for stPGOcc Object
summary.svcMsPGOcc | Methods for svcMsPGOcc Object
summary.svcPGBinom | Methods for svcPGBinom Object
summary.svcPGOcc | Methods for svcPGOcc Object
summary.svcTIntPGOcc | Methods for svcTIntPGOcc Object
summary.svcTMsPGOcc | Methods for svcTMsPGOcc Object
summary.svcTPGBinom | Methods for svcTPGBinom Object
summary.svcTPGOcc | Methods for svcTPGOcc Object
summary.tIntPGOcc | Methods for tIntPGOcc Object
summary.tMsPGOcc | Methods for tMsPGOcc Object
summary.tPGOcc | Methods for tPGOcc Object
svcMsPGOcc | Function for Fitting Multi-Species Spatially-Varying Coefficient Occupancy Models
svcPGBinom | Function for Fitting Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables
svcPGOcc | Function for Fitting Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables
svcTIntPGOcc | Function for Fitting Multi-Season Single-Species Spatially-varying Coefficient Integrated Occupancy Models Using Polya-Gamma Latent Variables
svcTMsPGOcc | Function for Fitting Multi-Species Multi-Season Spatially-Varying Coefficient Occupancy Models
svcTPGBinom | Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables
svcTPGOcc | Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables

## -- T --

tIntPGOcc | Function for Fitting Multi-Season Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables
tMsPGOcc | Function for Fitting Multi-Species Multi-Season Occupancy Models
tPGOcc | Function for Fitting Multi-Season Single-Species Occupancy Models Using Polya-Gamma Latent Variables

## -- U --

updateMCMC | Update a spOccupancy or spAbundance model run with more MCMC iterations

## -- W --

waicOcc | Compute Widely Applicable Information Criterion for spOccupancy Model Objects