Package: plsRcox 1.7.7

plsRcox: Partial Least Squares Regression for Cox Models and Related Techniques

Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings <doi:10.1093/bioinformatics/btu660>, Bastien, P., Bertrand, F., Meyer N., Maumy-Bertrand, M. (2015), Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data, Bioinformatics, 31(3):397-404. Cross validation criteria were studied in <arxiv:1810.02962>, Bertrand, F., Bastien, Ph. and Maumy-Bertrand, M. (2018), Cross validating extensions of kernel, sparse or regular partial least squares regression models to censored data.

Authors:Frederic Bertrand [cre, aut], Myriam Maumy-Bertrand [aut]

plsRcox_1.7.7.tar.gz
plsRcox_1.7.7.zip(r-4.5)plsRcox_1.7.7.zip(r-4.4)
plsRcox_1.7.7.tgz(r-4.4-any)
plsRcox_1.7.7.tar.gz(r-4.5-noble)plsRcox_1.7.7.tar.gz(r-4.4-noble)
plsRcox_1.7.7.tgz(r-4.4-emscripten)
plsRcox.pdf |plsRcox.html
plsRcox/json (API)

# Install 'plsRcox' in R:
install.packages('plsRcox', repos = c('https://fbertran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fbertran/plsrcox/issues

Pkgdown site:https://fbertran.github.io

Datasets:

On CRAN:

5.10 score 4 stars 2 packages 53 scripts 767 downloads 2 mentions 24 exports 159 dependencies

Last updated 2 years agofrom:297fba5089. Checks:5 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 25 2025
R-4.5-winOKJan 25 2025
R-4.5-linuxOKJan 25 2025
R-4.4-winOKJan 25 2025
R-4.4-macOKJan 25 2025

Exports:coxDKpls2DRcoxDKplsDRcoxDKsplsDRcoxplscoxpls2coxpls2DRcoxpls3coxpls3DRcoxplsDRcoxsplsDRcv.autoplsRcoxcv.coxDKplsDRcv.coxDKsplsDRcv.coxplscv.coxplsDRcv.coxsplsDRcv.larsDRcv.plsRcoxDKplsRcoxDKplsRcoxmodelDR_coxphlarsDR_coxphplsRcoxplsRcoxmodel

Dependencies:abindbackportsbase64encBHBiocParallelbipartitebootbootstrapbroombslibcachemcarcarDatacheckmateclasscliclustercodacodetoolscolorspacecorpcorcowplotcpp11data.tableDerivdiagramdigestdoBydotCall64dplyrellipseevaluatefansifarverfastmapfieldsfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggrepelglobalsgluegridExtragsignalgtablehighrHmischtmlTablehtmltoolshtmlwidgetsigraphipredisobandjquerylibjsonlitekernlabKernSmoothknitrlabelinglambda.rlarslatticelavalifecyclelistenvlme4magrittrmapsMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixOmicsmodelrmultcompmunsellmvtnormnetworknlmenloptrnnetnumDerivparallellypbkrtestpermutepillarpkgconfigplsplsRglmplyrpolsplinepracmaprodlimprogressrpurrrquantregR6rappdirsrARPACKrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rglrisksetROCrlangrmarkdownrmetarmsrpartRSpectrarstudioapisandwichsassscalesshapesnasnowspamSparseMSQUAREMstatnet.commonstringistringrSuppDistssurvAUCsurvcompsurvivalsurvivalROCTH.datatibbletidyrtidyselecttinytexutf8vctrsveganviridisviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
plsRcox-package: Partial Least Squares Regression for Cox Models and Related TechniquesplsRcox-package
Fitting a Direct Kernel PLS model on the (Deviance) ResidualscoxDKpls2DR coxDKpls2DR.default coxDKpls2DR.formula
Fitting a Direct Kernel PLS model on the (Deviance) ResidualscoxDKplsDR coxDKplsDR.default coxDKplsDR.formula
Fitting a Direct Kernel sPLSR model on the (Deviance) ResidualscoxDKsplsDR coxDKsplsDR.default coxDKsplsDR.formula
Fitting a Cox-Model on PLSR componentscoxpls coxpls.default coxpls.formula
Fitting a Cox-Model on PLSR componentscoxpls2 coxpls2.default coxpls2.formula
Fitting a PLSR model on the (Deviance) Residualscoxpls2DR coxpls2DR.default coxpls2DR.formula
Fitting a Cox-Model on PLSR componentscoxpls3 coxpls3.default coxpls3.formula
Fitting a PLSR model on the (Deviance) Residualscoxpls3DR coxpls3DR.default coxpls3DR.formula
Fitting a PLSR model on the (Deviance) ResidualscoxplsDR coxplsDR.default coxplsDR.formula
Fitting a sPLSR model on the (Deviance) ResidualscoxsplsDR coxsplsDR.default coxsplsDR.formula
Cross-validating an autoplsRcox-Modelcv.autoplsRcox
Cross-validating a DKplsDR-Modelcv.coxDKplsDR
Cross-validating a DKsplsDR-Modelcv.coxDKsplsDR
Cross-validating a Cox-Model fitted on PLSR componentscv.coxpls
Cross-validating a plsDR-Modelcv.coxplsDR
Cross-validating a splsDR-Modelcv.coxsplsDR
Cross-validating a larsDR-Modelcv.larsDR
Cross-validating a plsRcox-Modelcv.plsRcox
Partial least squares Regression generalized linear modelsDKplsRcox DKplsRcoxmodel DKplsRcoxmodel.default DKplsRcoxmodel.formula
(Deviance) Residuals ComputationDR_coxph
Fitting a LASSO/LARS model on the (Deviance) ResidualslarsDR_coxph larsDR_coxph.default larsDR_coxph.formula
Microsat features and survival timesmicro.censure
Partial least squares Regression generalized linear modelsplsRcox plsRcoxmodel plsRcoxmodel.default plsRcoxmodel.formula
Print method for plsRcox modelspredict.plsRcoxmodel
Print method for plsRcox modelsprint.plsRcoxmodel
Print method for summaries of plsRcox modelsprint.summary.plsRcoxmodel
Summary method for plsRcox modelssummary.plsRcoxmodel
Imputed Microsat featuresXmicro.censure_compl_imp