# Hierarchical Model of Species Communities

## Documentation for package ‘Hmsc’ version 3.3-7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

alignPosterior | alignPosterior
biPlot | biPlot
c.Hmsc | Combine Posterior Samples of Several Hmsc Models
computeAssociations | computeAssociations
computeDataParameters | computeDataParameters
computeInitialParameters | computeInitialParameters
computePredictedValues | computePredictedValues
computeSAIR | computeSAIR
computeVariancePartitioning | computeVariancePartitioning
computeWAIC | computeWAIC
constructGradient | constructGradient
constructKnots | constructKnots
convertToCodaObject | convertToCodaObject
coralCombine | coralCombine
coralGetRareSpeciesPriors | coralGetRareSpeciesPriors
coralGetXDataExt | coralGetXDataExt
coralPlotBeta | coralPlotBeta
coralPredict | coralPredict
coralPreprocess | coralPreprocess
coralSplitToBatches | coralSplitToBatches
coralTrain | coralTrain
createPartition | createPartition
evaluateModelFit | evaluateModelFit
getPostEstimate | getPostEstimate
Hmsc | Hmsc
HmscRandomLevel | Create an 'Hmsc' random level
importPosteriorFromHPC | importPosteriorFromHPC
pcomputePredictedValues | computePredictedValues
plotBeta | plotBeta
plotGamma | plotGamma
plotGradient | plotGradient
plotVariancePartitioning | plotVariancePartitioning
poolMcmcChains | poolMcmcChains
predict.Hmsc | predict
predictLatentFactor | predictLatentFactor
prepareGradient | prepareGradient
sampleMcmc | sampleMCMC
samplePrior | samplePrior
setPriors | setPriors
setPriors.Hmsc | setPriors.Hmsc
setPriors.HmscRandomLevel | setPriors.HmscRandomLevel
TD | Simulated data and a fitted Hmsc model for a small species community.