Univariate and Multivariate Spatial Modeling of Species Abundance

[Up] [Top]

Documentation for package ‘spAbundance’ version 0.1.3

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