{ "_id": "6a104513acfb0bcc41c9e654", "Package": "csmpv", "Type": "Package", "Title": "Biomarker Confirmation, Selection, Modelling, Prediction, and\nValidation", "Version": "1.0.5", "Authors@R": "person(given = \"Aixiang\",\nfamily = \"Jiang\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"aijiang@bccrc.ca\",\ncomment = c(ORCID = \"0000-0002-6153-7595\"))", "Maintainer": "Aixiang Jiang ", "VignetteBuilder": "knitr", "Description": "There are diverse purposes such as biomarker confirmation,\nnovel biomarker discovery, constructing predictive models,\nmodel-based prediction, and validation. It handles binary,\ncontinuous, and time-to-event outcomes at the sample or patient\nlevel. - Biomarker confirmation utilizes established functions\nlike glm() from 'stats', coxph() from 'survival', surv_fit(),\nand ggsurvplot() from 'survminer'. - Biomarker discovery and\nvariable selection are facilitated by three LASSO-related\nfunctions LASSO2(), LASSO_plus(), and LASSO2plus(), leveraging\nthe 'glmnet' R package with additional steps. - Eight versatile\nmodeling functions are offered, each designed for predictive\nmodels across various outcomes and data types. 1) LASSO2(),\nLASSO_plus(), LASSO2plus(), and LASSO2_reg() perform variable\nselection using LASSO methods and construct predictive models\nbased on selected variables. 2) XGBtraining() employs 'XGBoost'\nfor model building and is the only function not involving\nvariable selection. 3) Functions like LASSO2_XGBtraining(),\nLASSOplus_XGBtraining(), and LASSO2plus_XGBtraining() combine\nLASSO-related variable selection with 'XGBoost' for model\nconstruction. - All models support prediction and validation,\nrequiring a testing dataset comparable to the training dataset.\nAdditionally, the package introduces XGpred() for risk\nprediction based on survival data, with the XGpred_predict()\nfunction available for predicting risk groups in new datasets.\nThe methodology is based on our new algorithms and various\nreferences: - Hastie et al. (1992, ISBN 0 534 16765-9), -\nTherneau et al. (2000, ISBN 0-387-98784-3), - Kassambara et al.\n(2021) , -\nFriedman et al. (2010) , - Simon et\nal. (2011) , - Harrell (2023)\n, - Harrell (2023)\n, - Chen and Guestrin\n(2016) , - Aoki et al. (2023)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://ajiangsfu.r-universe.dev", "Date/Publication": "2025-12-12 02:45:40 UTC", "RemoteUrl": "https://github.com/ajiangsfu/csmpv", "RemoteRef": "HEAD", "RemoteSha": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "Packaged": { "Date": "2026-05-11 06:18:36 UTC", "User": "root" }, "Author": "Aixiang Jiang [aut, cre, cph] (ORCID:\n)", "MD5sum": "209fd7b0fa934bdcc94b1fda1607ec7b", "_user": "ajiangsfu", "_type": "src", "_file": "csmpv_1.0.5.tar.gz", "_fileid": "b0f67a2da2d8746ac3e3ff158a10e67e034cc1f555a1c01ed6e1dc9c352e5d10", "_filesize": 5404476, "_sha256": "b0f67a2da2d8746ac3e3ff158a10e67e034cc1f555a1c01ed6e1dc9c352e5d10", "_created": "2026-05-11T06:18:36.000Z", "_published": "2026-05-22T11:59:15.203Z", "_distro": "noble", "_jobs": [ { 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"LASSO2plus" ] }, { "page": "LASSO2plus_XGBtraining", "title": "XGBoost Modeling after Variable Selection with LASSO2plus", "topics": [ "LASSO2plus_XGBtraining" ] }, { "page": "rms_model", "title": "A Wrapper for Building Predictive Models using the rms Package", "topics": [ "rms_model" ] }, { "page": "validation", "title": "Validate Model Predictions", "topics": [ "validation" ] }, { "page": "XGBtraining", "title": "A Wrapper Function for xgboost::xgboost", "topics": [ "XGBtraining" ] }, { "page": "XGBtraining_predict", "title": "Predicting XGBoost Model Scores and Performing Validation", "topics": [ "XGBtraining_predict" ] }, { "page": "XGpred", "title": "XGpred: Building Risk Classification Predictive Models using Survival Data", "topics": [ "XGpred" ] }, { "page": "XGpred_predict", "title": "Predicting Risk Group Classification for a New Data Set", "topics": [ "XGpred_predict" ] } ], "_readme": "https://github.com/ajiangsfu/csmpv/raw/HEAD/README.md", "_rundeps": [ "abind", 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Example data", "2. Biomarker confirmation/validation", "2.1 Binary outcome", "2.2 Continous outcome", "2.3 Time-to-event outcome", "3. Biomarker discovery with variable selection", "3.1 Variable selection with LASSO2", "3.1.1 Binary outcome", "3.1.2 Continuous outcome", "3.1.3 Time-to-event outcome", "3.2 Variable selection with LASSO2plus", "Binary outcome", "Continuous outcome", "Time-to-event outcome", "3.3. Variable selection with LASSO_plus", "4. Predictive model development", "4.1 LASSO2", "4.2 LASSO2 + regular regression", "4.3 LASSO_plus", "4.4 LASSO2plus", "4.5 XGBoost", "4.6 LASSO2 + XGBoost", "4.7 LASSO_plus + XGBoost", "4.8 LASSO2plus + XGBoost", "5. Model prediction", "5.1 LASSO2 prediction", "Binary ouctome", "Continuous ouctome", "Time-to-event ouctome", "5.2 LASSO2 + regular regression prediction", "5.3 LASSO_plus prediction", "5.4 LASSO2plus prediction", "5.5 XGBoost prediction", "5.6 LASSO2 + XGBoost prediction", "5.7 LASSO_plus + XGBoost prediction", "1) Binary ouctome", "2) Continuous ouctome", "3) Time-to-event ouctome", "5.8 LASSO2plus + XGBoost prediction", "6. (External) Model Validation", "6.1 LASSO2 validation", "6.2 LASSO2 + regular regression validation", "6.3 LASSO_plus validation", "6.4 LASSO2plus validation", "6.5 XGBoost validation", "6.6 LASSO2 + XGBoost validation", "6.7 LASSO_plus + XGBoost validation", "6.8 LASSO2plus + XGBoost validation", "7. All-in-one!", "8. Special modelling", "csmpv R package general information", "References" ], "created": "2025-12-12 02:45:40", "modified": "2025-12-12 02:45:40", "commits": 1 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "csmpv", "_universes": [ "ajiangsfu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-05-11T06:21:43.000Z", "distro": "noble", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "4a272737f8059ac8aa33afca619383b13f1b8c7103edc1b4247a42713a338ae1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.6.0", "os": "linux", "version": "1.0.5", "date": "2026-05-11T06:21:35.000Z", "distro": "noble", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "57905c31876fd14abdce49b365a77387af4c9381d3272efb4ffb029aee91621c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.5.3", "os": "mac", "version": "1.0.5", "date": "2026-05-11T06:20:52.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "986e62e5c63b05beed136a53678805ba77bbaac4847d5aedeedc50a092071c8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.6.0", "os": "mac", "version": "1.0.5", "date": "2026-05-11T06:21:13.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "6fef50823c2f1b76dd9c686196031fe1fab5fec197b199b6b3bcdfb73617f733", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.7.0", "os": "win", "version": "1.0.5", "date": "2026-05-11T06:20:24.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "b2e1dfec9ff7328d0d37604a91a6f862560cac8810ac07340673019139111519", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.5.3", "os": "win", "version": "1.0.5", "date": "2026-05-11T06:20:02.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "6ccdee0f8ff6aa968f21c951760c7b7e997bd46bc511622179d671a8691d1d46", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.6.0", "os": "win", "version": "1.0.5", "date": "2026-05-11T06:20:03.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "005e21cfc2806094ee0b3791bbb8ad0876064a9c11ef1cc540511b48edadc146", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.5", "date": "2026-05-22T11:58:57.000Z", "commit": "b2412c98713c2de96bcfbb3e525b4eefb03d6c35", "fileid": "ec0e08a9913353eeb75ff8ad362457c5e4e04082c8639a5f2c3e363934b91330", "status": "success", "buildurl": "https://github.com/r-universe/ajiangsfu/actions/runs/25653505105" } ] }