Files in CenterForStatistics-UGent/RCM

Fit row-column association models with the negative binomial distribution for the microbiome

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 inst/NEWS.md 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