{ "_id": "6a1d36a41d7bb097a0a3d2b0", "Package": "predtools", "Title": "Prediction Model Tools", "Version": "0.0.3", "Authors@R": "c(\nperson(given = \"Mohsen\",\nfamily = \"Sadatsafavi\",\nrole = c(\"aut\", \"cph\"),\nemail = \"msafavi@mail.ubc.ca\",\ncomment = c(ORCID = \"0000-0002-0419-7862\")),\nperson(\"Amin\", \"Adibi\", email = \"adibi@alumni.ubc.ca\", role = c(\"cre\"),\ncomment = c(ORCID = \"0000-0003-2748-4781\")),\nperson(\"Abdollah\", \"Safari\", email = \"asafari@mail.ubc.ca\", role = c(\"aut\")),\nperson(\"Tae Yoon\", \"Lee\", email = \"dlxodbs@mail.ubc.ca\", role = c(\"aut\"))\n)", "Description": "Provides additional functions for evaluating predictive\nmodels, including plotting calibration curves and model-based\nReceiver Operating Characteristic (mROC) based on Sadatsafavi\net al (2021) .", "License": "GPL", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "URL": "https://github.com/resplab/predtools", "BugReports": "https://github.com/resplab/predtools/issues", "VignetteBuilder": "knitr", "Repository": "https://resplab.r-universe.dev", "Date/Publication": "2023-06-16 16:26:00 UTC", "RemoteUrl": "https://github.com/resplab/predtools", "RemoteRef": "HEAD", "RemoteSha": "4d90f59c22485177c65cfae3778ec16ec48e950a", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 07:20:30 UTC", "User": "root" }, "Author": "Mohsen Sadatsafavi [aut, cph] (ORCID:\n),\nAmin Adibi [cre] (ORCID: ),\nAbdollah Safari [aut],\nTae Yoon Lee [aut]", "Maintainer": "Amin Adibi ", "MD5sum": "c246a10daf12642e4872e2a0e34ffee6", "_user": "resplab", "_type": "src", "_file": "predtools_0.0.3.tar.gz", "_fileid": "e586a30a37bf01611f93cb008220052070a8fed7881e9a81fbc24a2951c75dd0", "_filesize": 1286287, "_sha256": "e586a30a37bf01611f93cb008220052070a8fed7881e9a81fbc24a2951c75dd0", "_created": "2026-06-01T07:20:30.000Z", "_published": "2026-06-01T07:37:08.528Z", "_distro": "noble", "_jobs": [ { "job": 78804568262, "time": 166, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7325585479" }, { "job": 78804568265, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7325574354" }, { "job": 78804568254, "time": 183, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7325589860" }, { "job": 78804568214, "time": 139, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7325578178" }, { "job": 78804568268, "time": 230, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7325702999" }, { "job": 78804568316, "time": 287, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7325760912" }, { "job": 78804568245, "time": 140, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7325798653" }, { "job": 78804568258, "time": 298, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7325797443" }, { "job": 78804156801, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7325541262" }, { "job": 78804568207, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7325572273" }, { "job": 78804568341, "time": 116, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7325572597" }, { "job": 78804568240, "time": 117, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7325572415" }, { "job": 78804568269, "time": 126, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7325574978" } ], "_buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/resplab/predtools", "_commit": { "id": "4d90f59c22485177c65cfae3778ec16ec48e950a", "author": "Amin Adibi ", "committer": "GitHub ", "message": "Merge pull request #18 from tyhlee/patch-7\n\n", "time": 1686932760 }, "_maintainer": { "name": "Amin Adibi", "email": "adibi@alumni.ubc.ca", "login": "aminadibi", "description": "", "uuid": 20497354, "orcid": "0000-0003-2748-4781" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "RConics", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "resplab", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 11, "_contributors": [ { "user": "aminadibi", "count": 75, "uuid": 20497354 }, { "user": "shoodood", "count": 33, "uuid": 63941553 }, { "user": "tyhlee", "count": 9, "uuid": 21114305 }, { "user": "msadatsafavi", "count": 6, "uuid": 25162764 }, { "user": "ab-sa", "count": 5, "uuid": 10256202 } ], "_userbio": { "uuid": 49206837, "type": "organization", "name": "RESP", "description": "The Respiratory Evaluation Sciences Program (RESP) at the University of British Columbia" }, "_downloads": { "count": 501, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/predtools" }, "_devurl": "https://github.com/resplab/predtools", "_searchresults": 155, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/predtools.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/resplab/predtools", "_realowner": "resplab", "_cranurl": true, "_releases": [ { "version": "0.0.2", "date": "2021-10-05" }, { "version": "0.0.3", "date": "2023-06-06" } ], "_exports": [ "calc_mROC_stats", "calc_NB_moments", "calibration_plot", "evpi_val", "mAUC", "mROC", "mROC_analysis", "mROC_inference", "mu_max_trunc_bvn", "odds_adjust", "pred_summary_stat" ], "_datasets": [ { "name": "dev_data", "title": "model development data", "object": "dev_data", "class": [ "data.frame" ], "fields": [ "age", "severity", "sex", "comorbidity", "y" ], "rows": 500, "table": true, "tojson": true }, { "name": "gusto", "title": "Anonymized data from the gusto trial", "object": "gusto", "class": [ "data.frame" ], "fields": [ "day30", "sho", "hig", "dia", "hyp", "hrt", "ttr", "sex", "Killip", "age", "ste", "pulse", "sysbp", "ant", "miloc", "height", "weight", "pmi", "htn", "smk", "pan", "fam", "prevcvd", "prevcabg", "regl", "grpl", "grps", "tpa", "tx" ], "rows": 40830, "table": true, "tojson": true }, { "name": "val_data", "title": "model validation data", "object": "val_data", "class": [ "data.frame" ], "fields": [ "age", "severity", "sex", "comorbidity", "y" ], "rows": 400, "table": true, "tojson": true } ], "_help": [ { "page": "calc_mROC_stats", "title": "Calculates the absolute surface between the empirical and expected ROCs", "topics": [ "calc_mROC_stats" ] }, { "page": "calc_NB_moments", "title": "Calculates the first two moments of the bivariate distribution of NB_model and NB_all", "topics": [ "calc_NB_moments" ] }, { "page": "calibration_plot", "title": "Title Create calibration plot based on observed and predicted outcomes.", "topics": [ "calibration_plot" ] }, { "page": "dev_data", "title": "model development data", "topics": [ "dev_data" ] }, { "page": "evpi_val", "title": "EVPI (Expected Value of Perfect Information) for validation Takes a vector of mean and a 2X2 covariance matrix", "topics": [ "evpi_val" ] }, { "page": "gusto", "title": "Anonymized data from the gusto trial", "topics": [ "gusto" ] }, { "page": "mAUC", "title": "Takes in a mROC object and calculates the area under the curve", "topics": [ "mAUC" ] }, { "page": "mROC", "title": "Calculates mROC from the vector of predicted risks Takes in a vector of probabilities and returns mROC values (True positives, False Positives in an object of class mROC)", "topics": [ "mROC" ] }, { "page": "mROC_analysis", "title": "Main eROC analysis that plots ROC and eROC", "topics": [ "mROC_analysis" ] }, { "page": "mROC_inference", "title": "Statistical inference for comparing empirical and expected ROCs. If CI=TRUE then also returns pointwise CIs", "topics": [ "mROC_inference" ] }, { "page": "mu_max_trunc_bvn", "title": "Calculates the expected value of the maximum of two random variables with zero-truncated bivariate normal distribution Takes a vector of mean and a 2X2 covariance matrix", "topics": [ "mu_max_trunc_bvn" ] }, { "page": "odds_adjust", "title": "Title Update a prediction model for a binary outcome by multiplying a fixed odd-ratio to the predicted odds.", "topics": [ "odds_adjust" ] }, { "page": "pred_summary_stat", "title": "Title Estimate mean and variance of prediction based on model calibration output.", "topics": [ "pred_summary_stat" ] }, { "page": "val_data", "title": "model validation data", "topics": [ "val_data" ] } ], "_readme": "https://github.com/resplab/predtools/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "mvtnorm", "pillar", "pkgconfig", "pROC", "R6", "RColorBrewer", "RConics", "Rcpp", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "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": "calibPlot.Rmd", "filename": "calibPlot.html", "title": "Calibration Plot", "engine": "knitr::rmarkdown", "headings": [ "What is calibration plot?", "A step-by-step guide." ], "created": "2021-09-25 00:07:27", "modified": "2022-08-08 16:25:32", "commits": 3 }, { "source": "interceptAdj.Rmd", "filename": "interceptAdj.html", "title": "Intercept Adjustment", "engine": "knitr::rmarkdown", "headings": [ "What is intercept adjustment?", "A step-by-step guide." ], "created": "2021-09-24 02:01:43", "modified": "2022-07-08 21:18:37", "commits": 6 }, { "source": "mROC.Rmd", "filename": "mROC.html", "title": "Model-based ROC", "engine": "knitr::rmarkdown", "headings": [ "What is mROC?", "Installation", "How the package works", "A step-by-step guide.", "Important note: the statistical inference on comparing mROC and ROC cannot be used for internal validation. Such a test is made for external validation." ], "created": "2021-09-13 20:38:17", "modified": "2021-09-24 02:49:02", "commits": 4 }, { "source": "UNLI2D.Rmd", "filename": "UNLI2D.html", "title": "Unit Normal Loss Integral in Two Dimensions", "engine": "knitr::rmarkdown", "headings": [ "Background", "What is UNLI?", "UNLI with Application in VoI Analysis", "2D UNLI", "Tutorial", "Installation", "Set-up", "Simulated data", "EVPI calculation" ], "created": "2022-10-19 01:49:50", "modified": "2022-10-19 01:49:50", "commits": 1 } ], "_score": 7.611935625040123, "_indexed": true, "_nocasepkg": "predtools", "_universes": [ "resplab", "aminadibi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.3", "date": "2026-05-02T15:57:42.000Z", "distro": "noble", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "eed2458c7741eb7d278ba3dbf4993a1af31d3eff793746be37c9a4b1ea2212ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/25255759581" }, { "r": "4.7.0", "os": "linux", "version": "0.0.3", "date": "2026-06-01T07:23:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "b9cf1771cae0e620d3d5f5399dacef073f4c1cb6a96d5b39cab33af95426be1a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "linux", "version": "0.0.3", "date": "2026-06-01T07:23:26.000Z", "distro": "noble", "arch": "aarch64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "c0cd98810fa4b1daba9ea48b28acd53334d70b973f721877612f45885a6bb51a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "linux", "version": "0.0.3", "date": "2026-06-01T07:22:42.000Z", "distro": "noble", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "66b2ac37ff96fe333dae7fcf149b09c99d5e4946afe6d6c6adf0ffa6db95b315", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.5.3", "os": "mac", "version": "0.0.3", "date": "2026-06-01T07:30:06.000Z", "arch": "aarch64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "43276dd7936e5dd2aa92241723eeca73a98765735831f355f50d83b5735b0e5a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.5.3", "os": "mac", "version": "0.0.3", "date": "2026-06-01T07:33:19.000Z", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "0002f095aa4ccea8f41c0d6a2d9dd2a952ac3751efa183cb669512f97a9d8c7b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "mac", "version": "0.0.3", "date": "2026-06-01T07:36:00.000Z", "arch": "aarch64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "6ab50ea9a9bfec6ee906af4e5ba33a6cd61e5ff06e848f691f3d14a4ae3df3a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "mac", "version": "0.0.3", "date": "2026-06-01T07:35:25.000Z", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "6f1f739dd8e1851b0ceb6a4a60a74d1d2cbe7d0ac5d620b81dbdb0e587ed5a33", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.3", "date": "2026-06-01T07:22:44.000Z", "arch": "emscripten", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "a135a4d9fc7b2eecaf7e955b385757c18581eafdbc4d54c29d1b6f250ba5b51d", "status": "success", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.7.0", "os": "win", "version": "0.0.3", "date": "2026-06-01T07:21:52.000Z", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "f52d31041d53de9b5832397e6a82b7728185faaa64603c7c031f80b0a138db92", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.5.3", "os": "win", "version": "0.0.3", "date": "2026-06-01T07:21:51.000Z", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "c95a584d2e494b684599a09a9a2ba4aebe11a1b0475822431007146fc3362dfb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" }, { "r": "4.6.0", "os": "win", "version": "0.0.3", "date": "2026-06-01T07:22:01.000Z", "arch": "x86_64", "commit": "4d90f59c22485177c65cfae3778ec16ec48e950a", "fileid": "bc74a5e639a6647079caab6f2602c937adbbea6955e5356e2976f02940d76568", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/resplab/actions/runs/26740804359" } ] }