├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── HMSC.Rproj ├── LICENSE ├── NAMESPACE ├── R ├── Hmsc.R ├── HmscRandomLevel.R ├── alignPosterior.R ├── biPlot.R ├── c.Hmsc.R ├── combineParameters.R ├── computeAssociations.R ├── computeDataParameters.R ├── computeInitialParameters.R ├── computePredictedValues.R ├── computePredictedValuesParallel.R ├── computePredictor.HmscRandomLevel.R ├── computeSAIR.R ├── computeVariancePartitioning.R ├── computeWAIC.R ├── constructGradient.R ├── constructKnots.R ├── convertToCodaObject.r ├── coralCombine.R ├── coralGetRareSpeciesPriors.R ├── coralGetXDataExt.R ├── coralPlotBeta.R ├── coralPredict.R ├── coralPreprocess.R ├── coralSplitToBatches.R ├── coralTrain.R ├── createPartition.R ├── data.R ├── evaluateModelFit.R ├── getPostEstimate.R ├── importPosteriorFromHPC.R ├── plotBeta.R ├── plotGamma.R ├── plotGradient.R ├── plotVariancePartitioning.R ├── poolMcmcChains.R ├── predict.R ├── predictLatentFactor.R ├── prepareGradient.R ├── print.Hmsc.R ├── print.HmscRandomLevel.R ├── sampleMcmc.R ├── samplePrior.R ├── setPriors.Hmsc.R ├── setPriors.HmscRandomLevel.R ├── setPriors.R ├── updateAlpha.R ├── updateBetaLambda.R ├── updateBetaSel.R ├── updateEta.R ├── updateGamma2.R ├── updateGammaEta.R ├── updateGammaV.R ├── updateInvSigma.R ├── updateLambdaPriors.R ├── updateLatentLoadingOrder.R ├── updateNf.R ├── updateRho.R ├── updateZ.R ├── updatewRRR.R ├── updatewRRRPriors.R └── utils.R ├── README.md ├── data-raw └── simulateTestData.R ├── data └── TD.rda ├── inst ├── NEWS.md └── README.md ├── man ├── Hmsc-package.Rd ├── Hmsc.Rd ├── HmscRandomLevel.Rd ├── TD.Rd ├── alignPosterior.Rd ├── biPlot.Rd ├── c.Hmsc.Rd ├── computeAssociations.Rd ├── computeDataParameters.Rd ├── computeInitialParameters.Rd ├── computePredictedValues.Rd ├── computeSAIR.Rd ├── computeVariancePartitioning.Rd ├── computeWAIC.Rd ├── constructGradient.Rd ├── constructKnots.Rd ├── convertToCodaObject.Rd ├── coralCombine.Rd ├── coralGetRareSpeciesPriors.Rd ├── coralGetXDataExt.Rd ├── coralPlotBeta.Rd ├── coralPredict.Rd ├── coralPreprocess.Rd ├── coralSplitToBatches.Rd ├── coralTrain.Rd ├── createPartition.Rd ├── evaluateModelFit.Rd ├── getPostEstimate.Rd ├── importPosteriorFromHPC.Rd ├── plotBeta.Rd ├── plotGamma.Rd ├── plotGradient.Rd ├── plotVariancePartitioning.Rd ├── poolMcmcChains.Rd ├── predict.Hmsc.Rd ├── predictLatentFactor.Rd ├── prepareGradient.Rd ├── sampleMcmc.Rd ├── samplePrior.Rd ├── setPriors.Hmsc.Rd ├── setPriors.HmscRandomLevel.Rd └── setPriors.Rd ├── tests ├── Examples │ └── Hmsc-Ex.Rout.save ├── testthat.R └── testthat │ ├── test-WAIC.R │ ├── test-initialParameters.R │ ├── test-sampling.R │ ├── test-setHmsc.R │ ├── test-setPriors.R │ └── test-setRL.R └── vignettes ├── README ├── load_libraries.R ├── makedata.R ├── vignette_1_univariate.Rmd ├── vignette_1_univariate.pdf ├── vignette_1_univariate.pdf.asis ├── vignette_2_multivariate_low.Rmd ├── 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