Files in CenterForStatistics-UGent/RCM
Fit row-column association models with the negative binomial distribution for the microbiome
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/F_GramSchmidt.R
R/F_JacCol_constr.R
R/F_JacCol_constr_noLab.R
R/F_LR_nb.R
R/F_LR_nb_Jac.R
R/F_NBalphaInfl.R
R/F_NBcolInfl.R
R/F_NBjacobianAbunds.R
R/F_NBjacobianCol.R
R/F_NBjacobianColNP.R
R/F_NBjacobianLibSizes.R
R/F_NBjacobianPsi.R
R/F_NBjacobianRow.R
R/F_NBpsiInfl.R
R/F_NBrowInfl.R
R/F_RCM.R
R/F_RCM_NB.R
R/F_addOrthProjection.R
R/F_arrayProd.R
R/F_buildCentMat.R
R/F_buildConfMat.R
R/F_buildCovMat.R
R/F_buildDesign.R
R/F_checkAlias.R
R/F_constrCorresp.R
R/F_correctXMissingness.R
R/F_dLR_nb.R
R/F_dNBabunds.R
R/F_dNBlibSizes.R
R/F_dNBllcol.R
R/F_dNBllcolNP.R
R/F_dNBllcol_constr.R
R/F_dNBllcol_constr_noLab.R
R/F_dNBllrow.R
R/F_dNBpsis.R
R/F_data.R
R/F_deviances.R
R/F_ellipseCoord.R
R/F_estDisp.R
R/F_estNBparams.R
R/F_estNBparamsNoLab.R
R/F_estNPresp.R
R/F_extractCoord.R
R/F_extractE.R
R/F_filterConfounders.R
R/F_getDevMat.R
R/F_getDevianceRes.R
R/F_getDistCoord.R
R/F_getInflCol.R
R/F_getInflRow.R
R/F_getInt.R
R/F_getLogLik.R
R/F_getModelMat.R
R/F_getRowMat.R
R/F_heq_nb.R
R/F_heq_nb_jac.R
R/F_indentPlot.R
R/F_inertia.R
R/F_liks.R
R/F_permanova.R
R/F_plot.RCM.R
R/F_plotRespFun.R
R/F_residualPlot.R
R/F_respFunJacMat.R
R/F_respFunScoreMat.R
R/F_rowMultiply.R
R/F_seq_k.R
R/F_trimOnConfounders.R
README.Rmd
README.md
README_figs/README-plotCond-1.png
README_figs/README-plotNPTriplot-1.png
README_figs/README-plotRichness-1.png
README_figs/README-plotUnconstrainedRCMall-1.png
README_figs/README-plotUnconstrainedRCMallColour-1.png
README_figs/README-plotlin2cor-1.png
README_figs/README-plotlin3-1.png
README_figs/README-plotlin3Triplot-1.png
data/Zeller.RData
inst/CITATION
inst/NEWS.md
inst/fits/zellerFits.RData
man/GramSchmidt.Rd
man/JacCol_constr.Rd
man/JacCol_constr_noLab.Rd
man/LR_nb.Rd
man/LR_nb_Jac.Rd
man/NBalphaInfl.Rd
man/NBcolInfl.Rd
man/NBjacobianAbundsOld.Rd
man/NBjacobianColNP.Rd
man/NBjacobianColOld.Rd
man/NBjacobianLibSizes.Rd
man/NBjacobianPsi.Rd
man/NBjacobianRow.Rd
man/NBpsiInfl.Rd
man/NBrowInfl.Rd
man/RCM.Rd
man/RCM_NB.Rd
man/Zeller.Rd
man/addOrthProjection.Rd
man/arrayprod.Rd
man/buildCentMat.Rd
man/buildConfMat.Rd
man/buildConfMat.character.Rd
man/buildConfMat.data.frame.Rd
man/buildCovMat.Rd
man/buildDesign.Rd
man/checkAlias.Rd
man/constrCorresp.Rd
man/correctXMissingness.Rd
man/dLR_nb.Rd
man/dNBabundsOld.Rd
man/dNBlibSizes.Rd
man/dNBllcolNP.Rd
man/dNBllcolOld.Rd
man/dNBllcol_constr.Rd
man/dNBllcol_constr_noLab.Rd
man/dNBllrow.Rd
man/dNBpsis.Rd
man/deviances.Rd
man/ellipseCoord.Rd
man/estDisp.Rd
man/estNBparams.Rd
man/estNBparamsNoLab.Rd
man/estNPresp.Rd
man/extractCoord.Rd
man/extractE.Rd
man/filterConfounders.Rd
man/getDevMat.Rd
man/getDevianceRes.Rd
man/getDistCoord.Rd
man/getInflCol.Rd
man/getInflRow.Rd
man/getInt.Rd
man/getLogLik.Rd
man/getModelMat.Rd
man/getRowMat.Rd
man/heq_nb.Rd
man/heq_nb_jac.Rd
man/indentPlot.Rd
man/inertia.Rd
man/liks.Rd
man/permanova.Rd
man/plot.RCM.Rd
man/plotRespFun.Rd
man/residualPlot.Rd
man/respFunJacMat.Rd
man/respFunScoreMat.Rd
man/rowMultiply.Rd
man/seq_k.Rd
man/trimOnConfounders.Rd
tests/testthat.R
tests/testthat/test-ArrayProd.R
tests/testthat/test-RCMinput.R
tests/testthat/test-RCMoutput.R
tests/testthat/test-ResidualPlot.R
tests/testthat/test-checkAlias.R
tests/testthat/test-permanova.R
tests/testthat/test-plotRCM.R
tests/testthat/test-removeNA.R
tests/testthat/test-rowMultiply.R
tests/testthat/test-seq_k.R
vignettes/RCMvignette.Rmd
