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

Documentation for package ‘spOccupancy’ version 0.8.0

Help Pages

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