Files in hmsc-r/HMSC

Hierarchical Model of Species Communities

R/Hmsc.R R/HmscRandomLevel.R R/alignPosterior.R R/biPlot.R R/c.Hmsc.R R/combineParameters.R R/computeAssociations.R R/computeDataParameters.R R/computeInitialParameters.R R/computePredictedValues.R R/computePredictedValuesParallel.R R/computePredictor.HmscRandomLevel.R R/computeSAIR.R R/computeVariancePartitioning.R R/computeWAIC.R R/constructGradient.R R/constructKnots.R R/convertToCodaObject.r R/coralCombine.R R/coralGetRareSpeciesPriors.R R/coralGetXDataExt.R R/coralPlotBeta.R R/coralPredict.R R/coralPreprocess.R R/coralSplitToBatches.R R/coralTrain.R R/createPartition.R R/data.R R/evaluateModelFit.R R/getPostEstimate.R R/importPosteriorFromHPC.R R/plotBeta.R R/plotGamma.R R/plotGradient.R R/plotVariancePartitioning.R R/poolMcmcChains.R R/predict.R R/predictLatentFactor.R R/prepareGradient.R R/print.Hmsc.R R/print.HmscRandomLevel.R R/sampleMcmc.R R/samplePrior.R R/setPriors.Hmsc.R R/setPriors.HmscRandomLevel.R R/setPriors.R R/updateAlpha.R R/updateBetaLambda.R R/updateBetaSel.R R/updateEta.R R/updateGamma2.R R/updateGammaEta.R R/updateGammaV.R R/updateInvSigma.R R/updateLambdaPriors.R R/updateLatentLoadingOrder.R R/updateNf.R R/updateRho.R R/updateZ.R R/updatewRRR.R R/updatewRRRPriors.R README.md data-raw/simulateTestData.R inst/NEWS.md inst/README.md man/Hmsc-package.Rd man/Hmsc.Rd man/HmscRandomLevel.Rd man/TD.Rd man/alignPosterior.Rd man/biPlot.Rd man/c.Hmsc.Rd man/computeAssociations.Rd man/computeDataParameters.Rd man/computeInitialParameters.Rd man/computePredictedValues.Rd man/computeSAIR.Rd man/computeVariancePartitioning.Rd man/computeWAIC.Rd man/constructGradient.Rd man/constructKnots.Rd man/convertToCodaObject.Rd man/coralCombine.Rd man/coralGetRareSpeciesPriors.Rd man/coralGetXDataExt.Rd man/coralPlotBeta.Rd man/coralPredict.Rd man/coralPreprocess.Rd man/coralSplitToBatches.Rd man/coralTrain.Rd man/createPartition.Rd man/evaluateModelFit.Rd man/getPostEstimate.Rd man/importPosteriorFromHPC.Rd man/plotBeta.Rd man/plotGamma.Rd man/plotGradient.Rd man/plotVariancePartitioning.Rd man/poolMcmcChains.Rd man/predict.Hmsc.Rd man/predictLatentFactor.Rd man/prepareGradient.Rd man/sampleMcmc.Rd man/samplePrior.Rd man/setPriors.Hmsc.Rd man/setPriors.HmscRandomLevel.Rd man/setPriors.Rd tests/testthat.R tests/testthat/test-WAIC.R tests/testthat/test-initialParameters.R tests/testthat/test-sampling.R tests/testthat/test-setHmsc.R tests/testthat/test-setPriors.R tests/testthat/test-setRL.R vignettes/load_libraries.R vignettes/makedata.R vignettes/vignette_1_univariate.Rmd vignettes/vignette_1_univariate.pdf vignettes/vignette_2_multivariate_low.Rmd vignettes/vignette_2_multivariate_low.pdf vignettes/vignette_3_multivariate_high.Rmd vignettes/vignette_3_multivariate_high.pdf vignettes/vignette_4_spatial.Rmd vignettes/vignette_4_spatial.pdf vignettes/vignette_5_performance.Rmd vignettes/vignette_5_performance.pdf