# Univariate and Multivariate Spatial Modeling of Species Abundance

## Documentation for package ‘spAbundance’ version 0.2.1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B D F H L M N P S W

## -- A --

abund | Function for Fitting Univariate Abundance GLMMs

## -- B --

bbsData | Count data for six warbler species in Pennsylvania, USA
bbsPredData | Covariates and coordinates for prediction of relative warbler abundance in Pennsylvania, USA

## -- D --

dataNMixSim | Simulated repeated count data of 6 species across 225 sites
DS | Function for Fitting Single-Species Hierarchical Distance Sampling Models

## -- F --

fitted.abund | Extract Model Fitted Values for abund Object
fitted.DS | Extract Model Fitted Values for DS Object
fitted.lfMsAbund | Extract Model Fitted Values for lfMsAbund Object
fitted.lfMsDS | Extract Model Fitted Values for lfMsDS Object
fitted.lfMsNMix | Extract Model Fitted Values for lfMsNMix Object
fitted.msAbund | Extract Model Fitted Values for msAbund Object
fitted.msDS | Extract Model Fitted Values for msDS Object
fitted.msNMix | Extract Model Fitted Values for msNMix Object
fitted.NMix | Extract Model Fitted Values for NMix Object
fitted.sfMsAbund | Extract Model Fitted Values for sfMsAbund Object
fitted.sfMsDS | Extract Model Fitted Values for sfMsDS Object
fitted.sfMsNMix | Extract Model Fitted Values for sfMsNMix Object
fitted.spAbund | Extract Model Fitted Values for spAbund Object
fitted.spDS | Extract Model Fitted Values for spDS Object
fitted.spNMix | Extract Model Fitted Values for spNMix Object
fitted.svcAbund | Extract Model Fitted Values for svcAbund Object
fitted.svcMsAbund | Extract Model Fitted Values for svcMsAbund Object

## -- H --

hbefCount2015 | Count data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest

## -- L --

lfMsAbund | Function for Fitting Latent Factor Multivariate Abundance GLMMs
lfMsDS | Function for Fitting Latent Factor Multi-Species Hierarchical Distance Sampling Models
lfMsNMix | Function for Fitting Latent Factor Multi-species N-mixture Models

## -- M --

msAbund | Function for Fitting Multivariate Abundance GLMMs
msDS | Function for Fitting Multi-Species Hierarchical Distance Sampling Models
msNMix | Function for Fitting Multi-species N-mixture Models

## -- N --

neonDWP | Distance sampling data of 16 bird species observed in the Disney Wilderness Preserve in 2018 in Florida, USA
neonPredData | Land cover covariates and coordinates at a 1ha resolution across Disney Wilderness Preserve
NMix | Function for Fitting Single-Species N-mixture Models

## -- P --

plot.abund | Methods for abund Object
plot.DS | Methods for DS Object
plot.lfMsAbund | Methods for lfMsAbund Object
plot.lfMsDS | Methods for lfMsDS Object
plot.lfMsNMix | Methods for lfMsNMix Object
plot.msAbund | Methods for msAbund Object
plot.msDS | Methods for msDS Object
plot.msNMix | Methods for msNMix Object
plot.NMix | Methods for NMix Object
plot.sfMsAbund | Methods for sfMsAbund Object
plot.sfMsDS | Methods for sfMsDS Object
plot.sfMsNMix | Methods for sfMsNMix Object
plot.spAbund | Methods for spAbund Object
plot.spDS | Methods for spDS Object
plot.spNMix | Methods for spNMix Object
plot.svcAbund | Methods for svcAbund Object
plot.svcMsAbund | Methods for svcMsAbund Object
ppcAbund | Function for performing posterior predictive checks
predict.abund | Function for prediction at new locations for univariate GLMMs
predict.DS | Function for prediction at new locations for single-species hierarchical distance sampling models
predict.lfMsAbund | Function for prediction at new locations for latent factor multivariate GLMMs
predict.lfMsDS | Function for prediction at new locations for latent factor multi-species hierarchical distance sampling models
predict.lfMsNMix | Function for prediction at new locations for latent factor multi-species N-mixture models
predict.msAbund | Function for prediction at new locations for multivariate GLMMs
predict.msDS | Function for prediction at new locations for multi-species hierarchical distance sampling models
predict.msNMix | Function for prediction at new locations for multi-species N-mixture models
predict.NMix | Function for prediction at new locations for single-species N-mixture models
predict.sfMsAbund | Function for prediction at new locations for spatial factor multivariate GLMMs
predict.sfMsDS | Function for prediction at new locations for spatial factor multi-species hierarchical distance sampling models
predict.sfMsNMix | Function for prediction at new locations for spatial factor multi-species N-mixture models
predict.spAbund | Function for prediction at new locations for univariate spatial GLMMs
predict.spDS | Function for prediction at new locations for single-species spatially-explicit hierarchical distance sampling models
predict.spNMix | Function for prediction at new locations for single-species spatial N-mixture models
predict.svcAbund | Function for prediction at new locations for univariate Gaussian spatially-varying coefficient models
predict.svcMsAbund | Function for prediction at new locations for multivariate spatially-varying coefficient GLMMs
print.abund | Methods for abund Object
print.DS | Methods for DS Object
print.lfMsAbund | Methods for lfMsAbund Object
print.lfMsDS | Methods for lfMsDS Object
print.lfMsNMix | Methods for lfMsNMix Object
print.msAbund | Methods for msAbund Object
print.msDS | Methods for msDS Object
print.msNMix | Methods for msNMix Object
print.NMix | Methods for NMix Object
print.sfMsAbund | Methods for sfMsAbund Object
print.sfMsDS | Methods for sfMsDS Object
print.sfMsNMix | Methods for sfMsNMix Object
print.spAbund | Methods for spAbund Object
print.spDS | Methods for spDS Object
print.spNMix | Methods for spNMix Object
print.svcAbund | Methods for svcAbund Object
print.svcMsAbund | Methods for svcMsAbund Object

## -- S --

sfMsAbund | Function for Fitting Spatial Factor Multivariate Abundance GLMMs
sfMsDS | Function for Fitting Spatial Factor Multi-Species Hierarchical Distance Sampling Models
sfMsNMix | Function for Fitting Spatial Factor Multi-species N-mixture Models
simAbund | Simulate Univariate Data for Testing GLMMs
simDS | Simulate Single-Species Distance Sampling Data
simMsAbund | Simulate Multivariate Data for Testing GLMMs
simMsDS | Simulate Multi-Species Distance Sampling Data
simMsNMix | Simulate Multi-Species Repeated Count Data with Imperfect Detection
simNMix | Simulate Single-Species Count Data with Imperfect Detection
spAbund | Function for Fitting Univariate Spatial Abundance GLMs
spDS | Function for Fitting Single-Species Spatially-Explicit Hierarchical Distance Sampling Models
spNMix | Function for Fitting Single-Species Spatial N-Mixture Models
summary.abund | Methods for abund Object
summary.DS | Methods for DS Object
summary.lfMsAbund | Methods for lfMsAbund Object
summary.lfMsDS | Methods for lfMsDS Object
summary.lfMsNMix | Methods for lfMsNMix Object
summary.msAbund | Methods for msAbund Object
summary.msDS | Methods for msDS Object
summary.msNMix | Methods for msNMix Object
summary.NMix | Methods for NMix Object
summary.sfMsAbund | Methods for sfMsAbund Object
summary.sfMsDS | Methods for sfMsDS Object
summary.sfMsNMix | Methods for sfMsNMix Object
summary.spAbund | Methods for spAbund Object
summary.spDS | Methods for spDS Object
summary.spNMix | Methods for spNMix Object
summary.svcAbund | Methods for svcAbund Object
summary.svcMsAbund | Methods for svcMsAbund Object
svcAbund | Function for Fitting Univariate Spatialy-Varying Coefficient GLMMs
svcMsAbund | Function for Fitting Spatially-Varying Coefficient Multivariate Abundance GLMMs

## -- W --

waicAbund | Compute Widely Applicable Information Criterion for spAbundance Model Objects