{ "_id": "6a11766dacfb0bcc41cf939d", "Package": "bigPLScox", "Type": "Package", "Version": "0.8.1", "Date": "2025-11-15", "biocViews": "", "Title": "Partial Least Squares for Cox Models with Big Matrices", "Authors@R": "c(\nperson(given = \"Frederic\", family= \"Bertrand\", role = c(\"cre\", \"aut\"), email = \"frederic.bertrand@lecnam.net\", comment = c(ORCID = \"0000-0002-0837-8281\")),\nperson(given = \"Myriam\", family= \"Maumy-Bertrand\", role = c(\"aut\"), email = \"myriam.maumy@ehesp.fr\", comment = c(ORCID = \"0000-0002-4615-1512\")))", "Author": "Frederic Bertrand [cre, aut]\n(), Myriam\nMaumy-Bertrand [aut] ()", "Maintainer": "Frederic Bertrand ", "Description": "Provides Partial least squares Regression and various\nregular, sparse or kernel, techniques for fitting Cox models\nfor big data. Provides a Partial Least Squares (PLS) algorithm\nadapted to Cox proportional hazards models that works with\n'bigmemory' matrices without loading the entire dataset in\nmemory. Also implements a gradient-descent based solver for Cox\nproportional hazards models that works directly on 'bigmemory'\nmatrices. Bertrand and Maumy (2023)\n, and\n highlighted fitting and\ncross-validating PLS-based Cox models to censored big data.", "License": "GPL-3", "Encoding": "UTF-8", "URL": "https://fbertran.github.io/bigPLScox/,\nhttps://github.com/fbertran/bigPLScox", "BugReports": "https://github.com/fbertran/bigPLScox/issues", "Classification/MSC": "62N01, 62N02, 62N03, 62N99", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "SystemRequirements": "C++17", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nmake texlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev zlib1g-dev", "Repository": "https://fbertran.r-universe.dev", "Date/Publication": "2025-11-17 22:19:03 UTC", "RemoteUrl": "https://github.com/fbertran/bigplscox", "RemoteRef": "HEAD", "RemoteSha": "91f3b041cc74e56a10fa3c314fc787251607c623", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-23 09:33:43 UTC", "User": "root" }, "MD5sum": "70ce616d201b9b0d15890dc1440b498b", "_user": "fbertran", "_type": "src", "_file": "bigPLScox_0.8.1.tar.gz", "_fileid": "92409ff6b5d0c9b4136796cebe74dcce09407681ef332a2449648258c8c70ac1", "_filesize": 1295776, "_sha256": "92409ff6b5d0c9b4136796cebe74dcce09407681ef332a2449648258c8c70ac1", "_created": "2026-05-23T09:33:43.000Z", "_published": "2026-05-23T09:42:05.363Z", "_distro": "noble", "_jobs": [ { "job": 77512672745, "time": 322, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7176012548" }, { "job": 77512672732, "time": 295, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7176010019" }, { "job": 77512672738, "time": 334, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7176013592" }, { "job": 77512672752, "time": 385, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7176018389" }, { "job": 77512672759, "time": 145, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175996417" }, { "job": 77512672742, "time": 423, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7176022201" }, { "job": 77512672740, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175996968" }, { "job": 77512672755, "time": 298, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7176010471" }, { "job": 77512193965, "time": 589, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175982718" }, { "job": 77512672679, "time": 259, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7176006824" }, { "job": 77512672690, "time": 242, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7176005393" }, { "job": 77512672691, "time": 205, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7176001993" }, { "job": 77512672695, "time": 241, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7176005362" } ], "_buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/fbertran/bigplscox", "_commit": { "id": "91f3b041cc74e56a10fa3c314fc787251607c623", "author": "Frederic Bertrand ", "committer": "Frederic Bertrand ", "message": "Fixed url in description file.\n", "time": 1763417943 }, "_maintainer": { "name": "Frederic Bertrand", "email": "frederic.bertrand@lecnam.net", "login": "fbertran", "orcid": "0000-0002-0837-8281", "twitter": "@BertrandFrdric2", "description": "Full professor in statistical modelling and data science at the CNAM Paris, France", "uuid": 6714333 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "BH", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "bigmemory", "role": "LinkingTo" }, { "package": "bigmemory", "role": "Imports" }, { "package": "bigalgebra", "role": "Imports" }, { "package": "bigSurvSGD", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "kernlab", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "risksetROC", "role": "Imports" }, { "package": "rms", "role": "Imports" }, { "package": "sgPLS", "role": "Imports" }, { "package": "survAUC", "role": "Imports" }, { "package": "survcomp", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "bench", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "plsRcox", "role": "Suggests" }, { "package": "mvtnorm", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "fbertran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 18 }, { "week": "2025-44", "n": 20 }, { "week": "2025-45", "n": 1 }, { "week": "2025-46", "n": 5 }, { "week": "2025-47", "n": 1 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "fbertran", "count": 45, "uuid": 6714333 } ], "_userbio": { "uuid": 6714333, "type": "user", "name": "Frederic Bertrand", "description": "Full professor in statistical modelling and data science at the CNAM Paris, France" }, "_downloads": { "count": 214, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bigPLScox" }, "_devurl": "https://github.com/fbertran/bigplscox", "_pkgdown": "https://fbertran.github.io/bigPLScox/", "_searchresults": 11, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/bigPLScox.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fbertran/bigplscox", "_realowner": "fbertran", "_cranurl": true, "_releases": [ { "version": "0.6.0", "date": "2025-11-11" }, { "version": "0.8.1", "date": "2025-11-18" } ], "_exports": [ "Arith", "benchmark_deviance_residuals", "big_pls_cox", "big_pls_cox_fast", "big_pls_cox_gd", "big_pls_cox_transform", "bigscale", "bigSurvSGD.na.omit", "component_information", "computeDR", "cox_deviance_details", "cox_deviance_residuals", "cox_deviance_residuals_big", "cox_partial_deviance_big", "coxDKgplsDR", "coxDKsgplsDR", "coxDKspls_sgplsDR", "coxgpls", "coxgplsDR", "coxsgpls", "coxsgplsDR", "coxspls_sgpls", "coxspls_sgplsDR", "cv.big_pls_cox", "cv.big_pls_cox_gd", "cv.coxDKgplsDR", "cv.coxDKsgplsDR", "cv.coxDKspls_sgplsDR", "cv.coxgpls", "cv.coxgplsDR", "cv.coxsgpls", "cv.coxsgplsDR", "cv.coxspls_sgpls", "cv.coxspls_sgplsDR", "dataCox", "gd_diagnostics", "partialbigSurvSGDv0", "select_ncomp" ], "_datasets": [ { "name": "dCox_sim", "title": "Simulated survival dataset for Cox models", "object": "dCox_sim", "file": "dCox_sim.RData", "class": [ "data.frame" ], "fields": [ "id", "time", "status", "x.1", "x.2" ], "rows": 10000, "table": true, "tojson": true }, { "name": "micro.censure", "title": "Microsat features and survival times", "object": "micro.censure", "file": "micro.censure.RData", "class": [ "data.frame" ], "fields": [ "numpat", "D18S61", "D17S794", "D13S173", "D20S107", "TP53", "D9S171", "D8S264", "D5S346", "D22S928", "D18S53", "D1S225", "D3S1282", "D15S127", "D1S305", "D1S207", "D2S138", "D16S422", "D9S179", "D10S191", "D4S394", "D1S197", "D6S264", "D14S65", "D17S790", "D5S430", "D3S1283", "D4S414", "D8S283", "D11S916", "D2S159", "D16S408", "D6S275", "D10S192", "sexe", "Agediag", "Siege", "T", "N", "M", "STADE", "survyear", "DC" ], "rows": 117, "table": true, "tojson": true }, { "name": "sim_data", "title": "Simulated dataset", "object": "sim_data", "file": "sim_data.RData", "class": [ "data.frame" ], "fields": [ "status", "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Xmicro.censure_compl_imp", "title": "Imputed Microsat features", "object": "Xmicro.censure_compl_imp", "file": "Xmicro.censure_compl_imp.RData", "class": [ "data.frame" ], "fields": [ "D18S61", "D17S794", "D13S173", "D20S107", "TP53", "D9S171", "D8S264", "D5S346", "D22S928", "D18S53", "D1S225", "D3S1282", "D15S127", "D1S305", "D1S207", "D2S138", "D16S422", "D9S179", "D10S191", "D4S394", "D1S197", "D6S264", "D14S65", "D17S790", "D5S430", "D3S1283", "D4S414", "D8S283", "D11S916", "D2S159", "D16S408", "D6S275", "D10S192", "sexe", "Agediag", "Siege", "T", "N", "M", "STADE" ], "rows": 117, "table": true, "tojson": true } ], "_help": [ { "page": "bigPLScox-package", "title": "bigPLScox-package", "topics": [ "bigPLScox-package", "bigPLScox" ] }, { "page": "align_big_plscox", "title": "Align a GD fit to a PLS fit (optional refit)", "topics": [ "align_big_plscox" ] }, { "page": "big_pls_cox", "title": "Partial Least Squares Components for Cox Models with Big Matrices", "topics": [ "big_pls_cox" ] }, { "page": "big_pls_cox_fast", "title": "Partial Least Squares Components for Cox Models (fast backend)", "topics": [ "big_pls_cox_fast" ] }, { "page": "big_pls_cox_gd", "title": "Gradient based PLS Cox for big matrices", "topics": [ "big_pls_cox_gd" ] }, { "page": "big_pls_cox_transform", "title": "Transform new data to PLS–Cox scores", "topics": [ "big_pls_cox_transform" ] }, { "page": "bigmatrix-operations", "title": "Matrix and arithmetic operations for big.matrix objects", "topics": [ "%*%,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" ] }, { "page": "bigscale", "title": "Construct Scaled Design Matrices for Big Survival Models", "topics": [ "bigscale" ] }, { "page": "bigSurvSGD.na.omit", "title": "Fit Survival Models with Stochastic Gradient Descent", "topics": [ "bigSurvSGD.na.omit" ] }, { "page": "component_information", "title": "Information criteria for component selection", "topics": [ "component_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" ] }, { "page": "computeDR", "title": "Compute deviance residuals", "topics": [ "computeDR" ] }, { "page": "cox_deviance_residuals", "title": "Cox deviance residuals via C++ backends", "topics": [ "benchmark_deviance_residuals", "cox_deviance_details", "cox_deviance_residuals", "cox_deviance_residuals_big", "cox_partial_deviance_big" ] }, { "page": "coxDKgplsDR", "title": "Fitting a Direct Kernel group PLS model on the (Deviance) Residuals", "topics": [ "coxDKgplsDR", "coxDKgplsDR.default", "coxDKgplsDR.formula" ] }, { "page": "coxDKsgplsDR", "title": "Fitting a Direct Kernel group sparse PLS model on the (Deviance) Residuals", "topics": [ "coxDKsgplsDR", "coxDKsgplsDR.default", "coxDKsgplsDR.formula" ] }, { "page": "coxDKspls_sgplsDR", "title": "Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals", "topics": [ "coxDKspls_sgplsDR", "coxDKspls_sgplsDR.default", "coxDKspls_sgplsDR.formula" ] }, { "page": "coxgpls", "title": "Fitting a Cox-Model on group PLSR components", "topics": [ "coxgpls", "coxgpls.default", "coxgpls.formula" ] }, { "page": "coxgplsDR", "title": "Fitting a Cox-Model on group PLSR components using the (Deviance) Residuals", "topics": [ "coxgplsDR", "coxgplsDR.default", "coxgplsDR.formula" ] }, { "page": "coxsgpls", "title": "Fitting a Cox-Model on group sparse PLSR components", "topics": [ "coxsgpls", "coxsgpls.default", "coxsgpls.formula" ] }, { "page": "coxsgplsDR", "title": "Fitting a Cox-Model on group sparse PLSR components using the (Deviance) Residuals", "topics": [ "coxsgplsDR", "coxsgplsDR.default", "coxsgplsDR.formula" ] }, { "page": "coxspls_sgpls", "title": "Fitting a Cox-Model on sparse PLSR components", "topics": [ "coxspls_sgpls", "coxspls_sgpls.default", "coxspls_sgpls.formula" ] }, { "page": "coxspls_sgplsDR", "title": "Fitting a Cox-Model on sparse PLSR components using the (Deviance) Residuals", "topics": [ "coxspls_sgplsDR", "coxspls_sgplsDR.default", "coxspls_sgplsDR.formula" ] }, { "page": "cv.big_pls_cox", "title": "Cross-validation for big-memory PLS-Cox models", "topics": [ "cv.big_pls_cox", "cv.big_pls_cox_gd" ] }, { "page": "cv.coxDKgplsDR", "title": "Cross-validating a Direct Kernel group PLS model fitted on the (Deviance) Residuals", "topics": [ "cv.coxDKgplsDR" ] }, { "page": "cv.coxDKsgplsDR", "title": "Cross-validating a Direct Kernel group sparse PLS model fitted on the (Deviance) Residuals", "topics": [ "cv.coxDKsgplsDR" ] }, { "page": "cv.coxDKspls_sgplsDR", "title": "Cross-validating a Direct Kernel sparse PLS model fitted on the (Deviance) Residuals", "topics": [ "cv.coxDKspls_sgplsDR" ] }, { "page": "cv.coxgpls", "title": "Cross-validating a Cox-Model fitted on group PLSR components", "topics": [ "cv.coxgpls" ] }, { "page": "cv.coxgplsDR", "title": "Cross-validating a Cox-Model fitted on group PLSR components using (Deviance) Residuals", "topics": [ "cv.coxgplsDR" ] }, { "page": "cv.coxsgpls", "title": "Cross-validating a Cox-Model fitted on sparse group PLSR components", "topics": [ "cv.coxsgpls" ] }, { "page": "cv.coxsgplsDR", "title": "Cross-validating a Cox-Model fitted on sparse group PLSR components using (Deviance) Residuals", "topics": [ "cv.coxsgplsDR" ] }, { "page": "cv.coxspls_sgpls", "title": "Cross-validating a Cox-Model fitted on sparse PLSR components", "topics": [ "cv.coxspls_sgpls" ] }, { "page": "cv.coxspls_sgplsDR", "title": "Cross-validating a Cox-Model fitted on sparse PLSR components components using (Deviance) Residuals", "topics": [ "cv.coxspls_sgplsDR" ] }, { "page": "dataCox", "title": "Cox Proportional Hazards Model Data Generation From Weibull Distribution", "topics": [ "dataCox" ] }, { "page": "dCox_sim", "title": "Simulated survival dataset for Cox models", "topics": [ "dCox_sim" ] }, { "page": "gd_diagnostics", "title": "Extract Diagnostics from a big_pls_cox_gd Model", "topics": [ "gd_diagnostics" ] }, { "page": "micro.censure", "title": "Microsat features and survival times", "topics": [ "micro.censure" ] }, { "page": "partialbigSurvSGDv0", "title": "Incremental Survival Model Fitting with Pre-Scaled Data", "topics": [ "partialbigSurvSGDv0" ] }, { "page": "plot.big_pls_cox", "title": "Plot method for big_pls_cox objects", "topics": [ "plot.big_pls_cox" ] }, { "page": "plot.big_pls_cox_gd", "title": "Plot method for big_pls_cox_gd objects", "topics": [ "plot.big_pls_cox_gd" ] }, { "page": "predict_cox_pls", "title": "Predict survival summaries from legacy Cox-PLS fits", "topics": [ "predict.coxDKgplsDR", "predict.coxDKsgplsDR", "predict.coxDKspls_sgplsDR", "predict.coxgpls", "predict.coxgplsDR", "predict.coxsgpls", "predict.coxsgplsDR", "predict.coxspls_sgpls", "predict_cox_pls" ] }, { "page": "predict_pls_latent", "title": "Predict responses and latent scores from PLS fits", "topics": [ "predict.gPLS", "predict.pls.cox", "predict.sgPLS", "predict.sPLS", "predict_pls_latent" ] }, { "page": "predict.big_pls_cox", "title": "Predict method for big-memory PLS-Cox models", "topics": [ "predict.big_pls_cox" ] }, { "page": "predict.big_pls_cox_fast", "title": "Predictions for fast big PLS–Cox fits", "topics": [ "predict.big_pls_cox_fast" ] }, { "page": "predict.big_pls_cox_gd", "title": "Predict method for big_pls_cox_gd", "topics": [ "predict.big_pls_cox_gd" ] }, { "page": "print.big_pls_cox", "title": "Print method for big_pls_cox objects", "topics": [ "print.big_pls_cox" ] }, { "page": "print.big_pls_cox_gd", "title": "Print method for big_pls_cox_gd objects", "topics": [ "print.big_pls_cox_gd" ] }, { "page": "print.summary.big_pls_cox_fast", "title": "Print method for summary.big_pls_cox_fast objects", "topics": [ "print.summary.big_pls_cox_fast" ] }, { "page": "sim_data", "title": "Simulated dataset", "topics": [ "sim_data" ] }, { "page": "summary.big_pls_cox", "title": "Summary for big_pls_cox objects", "topics": [ "summary.big_pls_cox" ] }, { "page": "summary.big_pls_cox_fast", "title": "Summary for big_pls_cox objects", "topics": [ "summary.big_pls_cox_fast" ] }, { "page": "summary.big_pls_cox_gd", "title": "Summary for big_pls_cox_gd objects", "topics": [ "summary.big_pls_cox_gd" ] }, { "page": "Xmicro.censure_compl_imp", "title": "Imputed Microsat features", "topics": [ "Xmicro.censure_compl_imp" ] } ], "_readme": "https://github.com/fbertran/bigplscox/raw/HEAD/README.md", "_rundeps": [ "backports", "base64enc", "BH", "bigalgebra", "bigmemory", "bigmemory.sri", "bigSurvSGD", "BiocParallel", "bootstrap", "bslib", "cachem", "caret", "checkmate", "class", "cli", "clock", "cluster", "codetools", "colorspace", "corpcor", "cpp11", "data.table", "diagram", "digest", "doParallel", "dplyr", "e1071", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "ggplot2", "ggrepel", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "igraph", "ipred", "isoband", "iterators", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "labeling", "lambda.r", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "memoise", "mime", "mixOmics", "ModelMetrics", "multcomp", "mvtnorm", "nlme", "nnet", "numDeriv", "parallelly", "pillar", "pkgconfig", "plyr", "polspline", "pROC", "prodlim", "progressr", "proxy", "purrr", "quantreg", "R6", "rappdirs", "rARPACK", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "recipes", "reshape2", "rgl", "risksetROC", "rlang", "rmarkdown", "rmeta", "rms", "rpart", "RSpectra", "rstudioapi", "S7", "sandwich", "sass", "scales", "sgPLS", "shape", "snow", "SparseM", "sparsevctrs", "SQUAREM", "stringi", "stringr", "SuppDists", "survAUC", "survcomp", "survival", "survivalROC", "TH.data", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tinytex", "tzdb", "utf8", "uuid", "vctrs", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "bigPLScox-benchmarking.Rmd", "filename": "bigPLScox-benchmarking.html", "title": "Benchmarking bigPLScox", "author": "Frédéric Bertrand", "engine": "knitr::rmarkdown", "headings": [ "Motivation", "Dependencies", "Simulated data", "Running the benchmark", "Dense matrix comparison", "Big-memory comparison", "Visualising the results", "Exporting benchmark tables", "Additional scripts" ], "created": "2025-10-31 00:49:15", "modified": "2025-11-16 00:40:18", "commits": 8 }, { "source": "bigPLScox.Rmd", "filename": "bigPLScox.html", "title": "Fast big-memory workflows with bigPLScox", "author": "Frédéric Bertrand", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2025-10-31 00:49:15", "modified": "2025-11-16 00:40:18", "commits": 6 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting started with bigPLScox", "author": "Frédéric Bertrand", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2025-10-31 00:49:15", "modified": "2025-11-16 00:40:18", "commits": 7 } ], "_score": 4.9164539485499255, "_indexed": true, "_nocasepkg": "bigplscox", "_universes": [ "fbertran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.1", "date": "2026-05-23T09:38:24.000Z", "distro": "noble", "arch": "aarch64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "827f0d382c91bfa4b25ce5e81c2a08ee9680412856ef84ec5564c217440723ac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.7.0", "os": "linux", "version": "0.8.1", "date": "2026-05-23T09:37:51.000Z", "distro": "noble", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "3b2fc6ec15febe1bc678edd3f6a1019bb3dc0a09655d682a7dc6498b6b9ecd2f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "linux", "version": "0.8.1", "date": "2026-05-23T09:38:38.000Z", "distro": "noble", "arch": "aarch64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "d0c3b8b92cf3ed91a44ee7c768dd3f02cd2303419cd7e439a7278114e44f075b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "linux", "version": "0.8.1", "date": "2026-05-23T09:39:14.000Z", "distro": "noble", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "ab0edc1a58282eff35461ee8dfd9792d21c68a1cb2188b8d81b10999dedd1c98", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.5.3", "os": "mac", "version": "0.8.1", "date": "2026-05-23T09:35:59.000Z", "arch": "aarch64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "a7fd8062a9dc951ec1c80e959935670b710bff09f5d090a661c9cbd15ba68c41", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.5.3", "os": "mac", "version": "0.8.1", "date": "2026-05-23T09:38:38.000Z", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "245df2fb372f44d19fbafb906162c353f802533f0e616b13ea2bb60695c3d838", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "mac", "version": "0.8.1", "date": "2026-05-23T09:36:02.000Z", "arch": "aarch64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "8edf663429490401be5c7dcbc177109683e4d8cf470d1bf67d1592fd63ae55fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "mac", "version": "0.8.1", "date": "2026-05-23T09:37:12.000Z", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "06b7592431ecc5865fd3bd8f9453b508db8a0eb779c8b40292ae22f9af35e99f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "wasm", "version": "0.8.1", "date": "2026-05-23T09:38:24.000Z", "arch": "emscripten", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "62e11d7d13cbbab3622603e8e453b90134838543bc5ad69bd87ce0959060ebd0", "status": "success", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.7.0", "os": "win", "version": "0.8.1", "date": "2026-05-23T09:36:09.000Z", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "eca2bc2458c4b57477d4c85c84b4b325e44d5237bcd414697cc147c2dcf5e738", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.5.3", "os": "win", "version": "0.8.1", "date": "2026-05-23T09:35:53.000Z", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "3bf437673c24370ed5b70fdfc248dca41d6f25e5f742aea7b942073d7e1f591a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" }, { "r": "4.6.0", "os": "win", "version": "0.8.1", "date": "2026-05-23T09:36:02.000Z", "arch": "x86_64", "commit": "91f3b041cc74e56a10fa3c314fc787251607c623", "fileid": "73a5219fbc03ab0c27f6e661c744ae75f09c5c7cbf0824a07071b6f6432ab170", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26329190870" } ] }