Function reference • spOccupancy

Package overview

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

Single-species models

PGOcc(): Function for Fitting Single-Species Occupancy Models Using Polya-Gamma Latent Variables

spPGOcc(): Function for Fitting Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables

intPGOcc(): Function for Fitting Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables

spIntPGOcc(): Function for Fitting Single-Species Integrated Spatial Occupancy Models Using Polya-Gamma Latent Variables

tPGOcc(): Function for Fitting Multi-Season Single-Species Occupancy Models Using Polya-Gamma Latent Variables

stPGOcc(): Function for Fitting Multi-Season Single-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables

svcPGOcc(): Function for Fitting Single-Species Spatially-Varying Coefficient Occupancy Models Using Polya-Gamma Latent Variables

svcPGBinom(): Function for Fitting 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

svcTPGBinom(): Function for Fitting Multi-Season Single-Species Spatially-Varying Coefficient Binomial Models Using Polya-Gamma Latent Variables

tIntPGOcc(): Function for Fitting Multi-Season Single-Species Integrated Occupancy Models Using Polya-Gamma Latent Variables

stIntPGOcc(): Function for Fitting Multi-Season Single-Species Spatial Integrated 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

Multi-species models

msPGOcc(): Function for Fitting Multi-Species Occupancy Models Using Polya-Gamma Latent Variables

spMsPGOcc(): Function for Fitting Multi-Species Spatial Occupancy Models Using Polya-Gamma Latent Variables

lfJSDM(): Function for Fitting a Latent Factor Joint Species Distribution Model

sfJSDM(): Function for Fitting a Spatial Factor Joint Species Distribution Model

lfMsPGOcc(): Function for Fitting Latent Factor Multi-Species Occupancy Models

sfMsPGOcc(): Function for Fitting Spatial Factor Multi-Species Occupancy Models

intMsPGOcc(): Function for Fitting Integrated Multi-Species Occupancy Models Using Polya-Gamma Latent Variables

tMsPGOcc(): Function for Fitting Multi-Species Multi-Season Occupancy Models

stMsPGOcc(): Function for Fitting Multi-Species Multi-Season Spatial Occupancy Models

svcMsPGOcc(): Function for Fitting Multi-Species Spatially-Varying Coefficient Occupancy Models

svcTMsPGOcc(): Function for Fitting Multi-Species Multi-Season Spatially-Varying Coefficient Occupancy Models

Goodness of Fit and Model Assessment

ppcOcc(): Function for performing posterior predictive checks

waicOcc(): Compute Widely Applicable Information Criterion for spOccupancy Model Objects

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

Data Simulation

simOcc(): Simulate Single-Species Detection-Nondetection Data

simMsOcc(): Simulate Multi-Species Detection-Nondetection Data

simIntOcc(): Simulate Single-Species Detection-Nondetection Data from Multiple Data Sources

simTOcc(): Simulate Multi-Season Single-Species Detection-Nondetection Data

simBinom(): Simulate Single-Species Binomial Data

simTBinom(): Simulate Multi-Season Single-Species Binomial Data

simIntMsOcc(): Simulate Multi-Species Detection-Nondetection Data from Multiple Data Sources

simTMsOcc(): Simulate Multi-Species Multi-Season Detection-Nondetection Data

simTIntOcc(): Simulate Single-Species Multi-Season Detection-Nondetection Data from Multiple Data Sources

Miscellaneous

postHocLM(): Function for Fitting Linear Mixed Models with Previous Model Estimates

getSVCSamples(): Extract spatially-varying coefficient MCMC samples

updateMCMC(): Update a spOccupancy or spAbundance model run with more MCMC iterations

Summary

summary(<PGOcc>) print(<PGOcc>) plot(<PGOcc>): Methods for PGOcc Object

summary(<spPGOcc>) print(<spPGOcc>) plot(<spPGOcc>): Methods for spPGOcc Object

summary(<msPGOcc>) print(<msPGOcc>) plot(<msPGOcc>): Methods for msPGOcc Object

summary(<spMsPGOcc>) print(<spMsPGOcc>) plot(<spMsPGOcc>): Methods for spMsPGOcc Object

summary(<intPGOcc>) print(<intPGOcc>) plot(<intPGOcc>): Methods for intPGOcc Object

summary(<spIntPGOcc>) print(<spIntPGOcc>) plot(<spIntPGOcc>): Methods for spIntPGOcc Object

summary(<lfJSDM>) print(<lfJSDM>) plot(<lfJSDM>): Methods for lfJSDM Object

summary(<sfJSDM>) print(<sfJSDM>) plot(<sfJSDM>): Methods for sfJSDM Object

summary(<lfMsPGOcc>) print(<lfMsPGOcc>) plot(<lfMsPGOcc>): Methods for lfMsPGOcc Object

summary(<sfMsPGOcc>) print(<sfMsPGOcc>) plot(<sfMsPGOcc>): Methods for sfMsPGOcc Object

summary(<tPGOcc>) print(<tPGOcc>) plot(<tPGOcc>): Methods for tPGOcc Object

summary(<stPGOcc>) print(<stPGOcc>) plot(<stPGOcc>): Methods for stPGOcc Object

summary(<ppcOcc>): Methods for ppcOcc Object

summary(<svcPGOcc>) print(<svcPGOcc>) plot(<svcPGOcc>): Methods for svcPGOcc Object

summary(<svcPGBinom>) print(<svcPGBinom>) plot(<svcPGBinom>): Methods for svcPGBinom Object

summary(<svcTPGOcc>) print(<svcTPGOcc>) plot(<svcTPGOcc>): Methods for svcTPGOcc Object

summary(<svcTPGBinom>) print(<svcTPGBinom>) plot(<svcTPGBinom>): Methods for svcTPGBinom Object

summary(<intMsPGOcc>) print(<intMsPGOcc>) plot(<intMsPGOcc>): Methods for intMsPGOcc Object

summary(<postHocLM>) print(<postHocLM>): Methods for postHocLM Object

summary(<svcMsPGOcc>) print(<svcMsPGOcc>) plot(<svcMsPGOcc>): Methods for svcMsPGOcc Object

summary(<tMsPGOcc>) print(<tMsPGOcc>) plot(<tMsPGOcc>): Methods for tMsPGOcc Object

summary(<stMsPGOcc>) print(<stMsPGOcc>) plot(<stMsPGOcc>): Methods for stMsPGOcc Object

summary(<svcTMsPGOcc>) print(<svcTMsPGOcc>) plot(<svcTMsPGOcc>): Methods for svcTMsPGOcc Object

summary(<tIntPGOcc>) print(<tIntPGOcc>) plot(<tIntPGOcc>): Methods for tIntPGOcc Object

summary(<stIntPGOcc>) print(<stIntPGOcc>) plot(<stIntPGOcc>): Methods for stIntPGOcc Object

summary(<svcTIntPGOcc>) print(<svcTIntPGOcc>) plot(<svcTIntPGOcc>): Methods for svcTIntPGOcc Object

Prediction

predict(<PGOcc>): Function for prediction at new locations for single-species occupancy models

predict(<spPGOcc>): Function for prediction at new locations for single-species spatial occupancy models

predict(<msPGOcc>): Function for prediction at new locations for multi-species occupancy models

predict(<spMsPGOcc>): Function for prediction at new locations for multi-species spatial occupancy models

predict(<intPGOcc>): Function for prediction at new locations for single-species integrated occupancy models

predict(<spIntPGOcc>): Function for prediction at new locations for single-species integrated spatial occupancy models

predict(<lfJSDM>): Function for prediction at new locations for latent factor joint species distribution models

predict(<sfJSDM>): Function for prediction at new locations for spatial factor joint species distribution model

predict(<lfMsPGOcc>): Function for prediction at new locations for latent factor multi-species occupancy models

predict(<sfMsPGOcc>): Function for prediction at new locations for spatial factor multi-species occupancy models

predict(<tPGOcc>): Function for prediction at new locations for multi-season single-species occupancy models

predict(<stPGOcc>): Function for prediction at new locations for multi-season single-species spatial occupancy models

predict(<svcPGOcc>): Function for prediction at new locations for single-species spatially-varying coefficient occupancy models

predict(<svcPGBinom>): Function for prediction at new locations for 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(<svcTPGBinom>): Function for prediction at new locations for multi-season single-species spatially-varying coefficient binomial models

predict(<intMsPGOcc>): Function for prediction at new locations for integrated multi-species occupancy models

predict(<svcMsPGOcc>): Function for prediction at new locations for spatially varying coefficient multi-species occupancy models

predict(<tMsPGOcc>): Function for prediction at new locations for multi-season multi-species occupancy models

predict(<stMsPGOcc>): Function for prediction at new locations for multi-season multi-species spatial occupancy models

predict(<svcTMsPGOcc>): Function for prediction at new locations for multi-season multi-species spatially-varying coefficient occupancy models

predict(<tIntPGOcc>): Function for prediction at new locations for multi-season single-species integrated occupancy models

predict(<stIntPGOcc>): Function for prediction at new locations for multi-season single-species spatial integrated occupancy models

predict(<svcTIntPGOcc>): Function for prediction at new locations for multi-season single-species spatially-varying coefficient integrated occupancy models

Fitted values

fitted(<PGOcc>): Extract Model Fitted Values for PGOcc Object

fitted(<spPGOcc>): Extract Model Fitted Values for spPGOcc Object

fitted(<msPGOcc>): Extract Model Fitted Values for msPGOcc Object

fitted(<spMsPGOcc>): Extract Model Fitted Values for spMsPGOcc Object

fitted(<intPGOcc>): Extract Model Fitted Values for intPGOcc Object

fitted(<spIntPGOcc>): Extract Model Fitted Values for spIntPGOcc Object

fitted(<lfJSDM>): Extract Model Fitted Values for lfJSDM Object

fitted(<sfJSDM>): Extract Model Fitted Values for sfJSDM Object

fitted(<lfMsPGOcc>): Extract Model Fitted Values for lfMsPGOcc Object

fitted(<sfMsPGOcc>): Extract Model Fitted Values for sfMsPGOcc Object

fitted(<tPGOcc>): Extract Model Fitted Values for tPGOcc Object

fitted(<stPGOcc>): Extract Model Fitted Values for stPGOcc Object

fitted(<svcPGOcc>): Extract Model Fitted Values for svcPGOcc Object

fitted(<svcPGBinom>): Extract Model Fitted Values for svcPGBinom Object

fitted(<svcTPGOcc>): Extract Model Fitted Values for svcTPGOcc Object

fitted(<svcTPGBinom>): Extract Model Fitted Values for svcTPGBinom Object

fitted(<svcMsPGOcc>): Extract Model Fitted Values for svcMsPGOcc Object

fitted(<tMsPGOcc>): Extract Model Fitted Values for tMsPGOcc Object

fitted(<stMsPGOcc>): Extract Model Fitted Values for stMsPGOcc Object

fitted(<svcTMsPGOcc>): Extract Model Fitted Values for svcTMsPGOcc Object

fitted(<tIntPGOcc>): Extract Model Fitted Values for tIntPGOcc Object

fitted(<stIntPGOcc>): Extract Model Fitted Values for stIntPGOcc Object

fitted(<svcTIntPGOcc>): Extract Model Fitted Values for svcTIntPGOcc Object

Data

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

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

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