Package: bigPLScox 0.8.1

bigPLScox: Partial Least Squares for Cox Models with Big Matrices

Provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models for big data. Provides a Partial Least Squares (PLS) algorithm adapted to Cox proportional hazards models that works with 'bigmemory' matrices without loading the entire dataset in memory. Also implements a gradient-descent based solver for Cox proportional hazards models that works directly on 'bigmemory' matrices. Bertrand and Maumy (2023) <https://hal.science/hal-05352069>, and <https://hal.science/hal-05352061> highlighted fitting and cross-validating PLS-based Cox models to censored big data.

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

bigPLScox_0.8.1.tar.gz
bigPLScox_0.8.1.zip(r-4.7)bigPLScox_0.8.1.zip(r-4.6)bigPLScox_0.8.1.zip(r-4.5)
bigPLScox_0.8.1.tgz(r-4.6-x86_64)bigPLScox_0.8.1.tgz(r-4.6-arm64)bigPLScox_0.8.1.tgz(r-4.5-x86_64)bigPLScox_0.8.1.tgz(r-4.5-arm64)
bigPLScox_0.8.1.tar.gz(r-4.7-arm64)bigPLScox_0.8.1.tar.gz(r-4.7-x86_64)bigPLScox_0.8.1.tar.gz(r-4.6-arm64)bigPLScox_0.8.1.tar.gz(r-4.6-x86_64)
bigPLScox_0.8.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bigPLScox/json (API)

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

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

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

openblascpp

4.92 score 1 stars 11 scripts 281 downloads 38 exports 147 dependencies

Last updated from:91f3b041cc. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK307
linux-devel-x86_64OK333
source / vignettesOK588
linux-release-arm64OK325
linux-release-x86_64OK343
macos-release-arm64OK208
macos-release-x86_64OK548
macos-oldrel-arm64OK187
macos-oldrel-x86_64OK502
windows-develOK272
windows-releaseOK307
windows-oldrelOK256
wasm-releaseOK245

Exports:Arithbenchmark_deviance_residualsbig_pls_coxbig_pls_cox_fastbig_pls_cox_gdbig_pls_cox_transformbigscalebigSurvSGD.na.omitcomponent_informationcomputeDRcox_deviance_detailscox_deviance_residualscox_deviance_residuals_bigcox_partial_deviance_bigcoxDKgplsDRcoxDKsgplsDRcoxDKspls_sgplsDRcoxgplscoxgplsDRcoxsgplscoxsgplsDRcoxspls_sgplscoxspls_sgplsDRcv.big_pls_coxcv.big_pls_cox_gdcv.coxDKgplsDRcv.coxDKsgplsDRcv.coxDKspls_sgplsDRcv.coxgplscv.coxgplsDRcv.coxsgplscv.coxsgplsDRcv.coxspls_sgplscv.coxspls_sgplsDRdataCoxgd_diagnosticspartialbigSurvSGDv0select_ncomp

Dependencies:backportsbase64encBHbigalgebrabigmemorybigmemory.sribigSurvSGDBiocParallelbootstrapbslibcachemcaretcheckmateclasscliclockclustercodetoolscolorspacecorpcorcpp11data.tablediagramdigestdoParalleldplyre1071ellipseevaluatefarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggrepelglobalsgluegowergridExtragtablehardhathighrHmischtmlTablehtmltoolshtmlwidgetsigraphipredisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglambda.rlatticelavalifecyclelistenvlubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemimemixOmicsModelMetricsmultcompmvtnormnlmennetnumDerivparallellypillarpkgconfigplyrpolsplinepROCprodlimprogressrproxypurrrquantregR6rappdirsrARPACKRColorBrewerRcppRcppArmadilloRcppEigenrecipesreshape2rglrisksetROCrlangrmarkdownrmetarmsrpartRSpectrarstudioapiS7sandwichsassscalessgPLSshapesnowSparseMsparsevctrsSQUAREMstringistringrSuppDistssurvAUCsurvcompsurvivalsurvivalROCTH.datatibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8uuidvctrsviridisLitewithrxfunyamlzoo

Benchmarking bigPLScox
Motivation | Dependencies | Simulated data | Running the benchmark | Dense matrix comparison | Big-memory comparison | Visualising the results | Exporting benchmark tables | Additional scripts
Rendered frombigPLScox-benchmarking.Rmdusingknitr::rmarkdown

Last update: 2025-11-16
Started: 2025-10-31

Fast big-memory workflows with bigPLScox
Introduction | Simulating a large survival dataset | Dense-matrix solvers | Switching to file-backed matrices | Gradient descent for streaming data | Comparing the latent subspaces | Predictions on new data | Timing snapshot | Cleaning up backing files | Cleaning up | Further resources
Rendered frombigPLScox.Rmdusingknitr::rmarkdown

Last update: 2025-11-16
Started: 2025-10-31

Getting started with bigPLScox
Why bigPLScox? | Loading the example data | Inspecting deviance residuals | Matrix-based PLS–Cox models | Cross-validation | Fast solvers for medium-sized data | Fast PLS Cox vs gradient based PLS Cox | Predictions and evaluation | DK-splines extension | Next steps
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2025-11-16
Started: 2025-10-31

Readme and manuals

Help Manual

Help pageTopics
bigPLScox-packagebigPLScox-package bigPLScox
Align a GD fit to a PLS fit (optional refit)align_big_plscox
Partial Least Squares Components for Cox Models with Big Matricesbig_pls_cox
Partial Least Squares Components for Cox Models (fast backend)big_pls_cox_fast
Gradient based PLS Cox for big matricesbig_pls_cox_gd
Transform new data to PLS–Cox scoresbig_pls_cox_transform
Matrix and arithmetic operations for big.matrix objects%*%,big.matrix,big.matrix-method %*%,big.matrix,matrix-method %*%,matrix,big.matrix-method Arith,big.matrix,big.matrix-method Arith,big.matrix,matrix-method Arith,big.matrix,numeric-method Arith,matrix,big.matrix-method Arith,numeric,big.matrix-method bigmatrix-operations
Construct Scaled Design Matrices for Big Survival Modelsbigscale
Fit Survival Models with Stochastic Gradient DescentbigSurvSGD.na.omit
Information criteria for component selectioncomponent_information component_information, component_information.big_pls_cox component_information.big_pls_cox, component_information.big_pls_cox_gd component_information.big_pls_cox_gd, select_ncomp
Compute deviance residualscomputeDR
Cox deviance residuals via C++ backendsbenchmark_deviance_residuals cox_deviance_details cox_deviance_residuals cox_deviance_residuals_big cox_partial_deviance_big
Fitting a Direct Kernel group PLS model on the (Deviance) ResidualscoxDKgplsDR coxDKgplsDR.default coxDKgplsDR.formula
Fitting a Direct Kernel group sparse PLS model on the (Deviance) ResidualscoxDKsgplsDR coxDKsgplsDR.default coxDKsgplsDR.formula
Fitting a Cox-Model on sparse PLSR components using the (Deviance) ResidualscoxDKspls_sgplsDR coxDKspls_sgplsDR.default coxDKspls_sgplsDR.formula
Fitting a Cox-Model on group PLSR componentscoxgpls coxgpls.default coxgpls.formula
Fitting a Cox-Model on group PLSR components using the (Deviance) ResidualscoxgplsDR coxgplsDR.default coxgplsDR.formula
Fitting a Cox-Model on group sparse PLSR componentscoxsgpls coxsgpls.default coxsgpls.formula
Fitting a Cox-Model on group sparse PLSR components using the (Deviance) ResidualscoxsgplsDR coxsgplsDR.default coxsgplsDR.formula
Fitting a Cox-Model on sparse PLSR componentscoxspls_sgpls coxspls_sgpls.default coxspls_sgpls.formula
Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residualscoxspls_sgplsDR coxspls_sgplsDR.default coxspls_sgplsDR.formula
Cross-validation for big-memory PLS-Cox modelscv.big_pls_cox cv.big_pls_cox_gd
Cross-validating a Direct Kernel group PLS model fitted on the (Deviance) Residualscv.coxDKgplsDR
Cross-validating a Direct Kernel group sparse PLS model fitted on the (Deviance) Residualscv.coxDKsgplsDR
Cross-validating a Direct Kernel sparse PLS model fitted on the (Deviance) Residualscv.coxDKspls_sgplsDR
Cross-validating a Cox-Model fitted on group PLSR componentscv.coxgpls
Cross-validating a Cox-Model fitted on group PLSR components using (Deviance) Residualscv.coxgplsDR
Cross-validating a Cox-Model fitted on sparse group PLSR componentscv.coxsgpls
Cross-validating a Cox-Model fitted on sparse group PLSR components using (Deviance) Residualscv.coxsgplsDR
Cross-validating a Cox-Model fitted on sparse PLSR componentscv.coxspls_sgpls
Cross-validating a Cox-Model fitted on sparse PLSR components components using (Deviance) Residualscv.coxspls_sgplsDR
Cox Proportional Hazards Model Data Generation From Weibull DistributiondataCox
Simulated survival dataset for Cox modelsdCox_sim
Extract Diagnostics from a big_pls_cox_gd Modelgd_diagnostics
Microsat features and survival timesmicro.censure
Incremental Survival Model Fitting with Pre-Scaled DatapartialbigSurvSGDv0
Plot method for big_pls_cox objectsplot.big_pls_cox
Plot method for big_pls_cox_gd objectsplot.big_pls_cox_gd
Predict survival summaries from legacy Cox-PLS fitspredict.coxDKgplsDR predict.coxDKsgplsDR predict.coxDKspls_sgplsDR predict.coxgpls predict.coxgplsDR predict.coxsgpls predict.coxsgplsDR predict.coxspls_sgpls predict_cox_pls
Predict responses and latent scores from PLS fitspredict.gPLS predict.pls.cox predict.sgPLS predict.sPLS predict_pls_latent
Predict method for big-memory PLS-Cox modelspredict.big_pls_cox
Predictions for fast big PLS–Cox fitspredict.big_pls_cox_fast
Predict method for big_pls_cox_gdpredict.big_pls_cox_gd
Print method for big_pls_cox objectsprint.big_pls_cox
Print method for big_pls_cox_gd objectsprint.big_pls_cox_gd
Print method for summary.big_pls_cox_fast objectsprint.summary.big_pls_cox_fast
Simulated datasetsim_data
Summary for big_pls_cox objectssummary.big_pls_cox
Summary for big_pls_cox objectssummary.big_pls_cox_fast
Summary for big_pls_cox_gd objectssummary.big_pls_cox_gd
Imputed Microsat featuresXmicro.censure_compl_imp