{ "_id": "6a1f2ffeb401979e7342769a", "Package": "calibmsm", "Title": "Calibration Plots for the Transition Probabilities from\nMultistate Models", "Version": "1.1.3", "Authors@R": "c(\nperson(given = \"Alexander\", family = \"Pate\", email = \"alexander.pate@manchester.ac.uk\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-0849-3458\")),\nperson(given = \"Glen P\", family = \"Martin\", email = \"glen.martin@manchester.ac.uk\", role = c(\"fnd\", \"rev\"),\ncomment = c(ORCID = \"0000-0002-3410-9472\"))\n)", "Description": "Assess the calibration of an existing (i.e. previously\ndeveloped) multistate model through calibration plots.\nCalibration is assessed using one of three methods. 1)\nCalibration methods for binary logistic regression models\napplied at a fixed time point in conjunction with inverse\nprobability of censoring weights. 2) Calibration methods for\nmultinomial logistic regression models applied at a fixed time\npoint in conjunction with inverse probability of censoring\nweights. 3) Pseudo-values estimated using the Aalen-Johansen\nestimator of observed risk. All methods are applied in\nconjunction with landmarking when required. These calibration\nplots evaluate the calibration (in a validation cohort of\ninterest) of the transition probabilities estimated from an\nexisting multistate model. While package development has\nfocused on multistate models, calibration plots can be produced\nfor any model which utilises information post baseline to\nupdate predictions (e.g. dynamic models); competing risks\nmodels; or standard single outcome survival models, where\npredictions can be made at any landmark time. Please see Pate\net al. (2024) and Pate et al. (2024)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "URL": "https://github.com/alexpate30/calibmsm,\nhttps://alexpate30.github.io/calibmsm/", "BugReports": "https://github.com/alexpate30/calibmsm/issues", "LazyData": "true", "VignetteBuilder": "knitr, R.rsp", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://alexpate30.r-universe.dev", "Date/Publication": "2026-04-15 12:43:48 UTC", "RemoteUrl": "https://github.com/alexpate30/calibmsm", "RemoteRef": "HEAD", "RemoteSha": "487de8d602609713628bea868f04c06f77896daa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 09:00:06 UTC", "User": "root" }, "Author": "Alexander Pate [aut, cre, cph] (ORCID:\n),\nGlen P Martin [fnd, rev] (ORCID:\n)", "Maintainer": "Alexander Pate ", "MD5sum": "08b4f7420f26624eb55a8539f30cd313", "_user": "alexpate30", "_type": "src", "_file": "calibmsm_1.1.3.tar.gz", "_fileid": "78bbf8de3b2ce79978de819bfe2b53a998ed13bc6298de3a2e6693319531fa4a", "_filesize": 2131048, "_sha256": "78bbf8de3b2ce79978de819bfe2b53a998ed13bc6298de3a2e6693319531fa4a", "_created": "2026-05-15T09:00:06.000Z", "_published": "2026-06-02T19:33:18.363Z", "_distro": "noble", "_jobs": [ { "job": 79155334411, "time": 425, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7013692303" }, { "job": 79155334305, "time": 461, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7013701935" }, { "job": 79155334690, "time": 480, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7013707441" }, { "job": 79155334177, "time": 480, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7013707351" }, { "job": 79155333659, "time": 233, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7013575250" }, { "job": 79155333693, "time": 158, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367863562" }, { "job": 79155334414, "time": 432, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7013694070" }, { "job": 79155334703, "time": 437, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7013695574" }, { "job": 79155334468, "time": 408, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7013687043" } ], "_buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/alexpate30/calibmsm", "_commit": { "id": "487de8d602609713628bea868f04c06f77896daa", "author": "alexpate30 ", "committer": "alexpate30 ", "message": "Update calibmsm.R\n\nImprove efficiency of code to extract which state individuals are in at time t (the outcome in validation dataset).\n\nOld version stored in calib_msm_old. Integrated tests should pick up any erros, but I will manually check to compare the two. This will help validate existing tests as well.\n", "time": 1776257028 }, "_maintainer": { "name": "Alexander Pate", "email": "alexander.pate@manchester.ac.uk", "login": "alexpate30", "uuid": 52957704, "orcid": "0000-0002-0849-3458" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "boot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "ggExtra", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "Hmisc", "role": "Imports" }, { "package": "mstate", "role": "Imports" }, { "package": "rms", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "VGAM", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "R.rsp", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "survminer", "role": "Suggests" }, { "package": "flexsurv", "role": "Suggests" } ], "_owner": "alexpate30", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 11 }, { "week": "2025-24", "n": 3 }, { "week": "2026-16", "n": 5 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "alexpate30", "count": 355, "uuid": 52957704 } ], "_userbio": { "uuid": 52957704, "type": "user", "name": "alexpate30" }, "_downloads": { "count": 221, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/calibmsm" }, "_devurl": "https://github.com/alexpate30/calibmsm", "_pkgdown": "https://alexpate30.github.io/calibmsm/", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/calibmsm.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/alexpate30/calibmsm", "_realowner": "alexpate30", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-11-30" }, { "version": "1.1.0", "date": "2024-05-13" }, { "version": "1.1.1", "date": "2024-06-14" }, { "version": "1.1.2", "date": "2025-06-06" }, { "version": "1.1.3", "date": "2025-06-13" } ], "_exports": [ "calc_weights", "calib_msm", "metadata" ], "_datasets": [ { "name": "ebmtcal", "title": "European Group for Blood and Marrow Transplantation data (one row per individual)", "object": "ebmtcal", "class": [ "data.frame" ], "fields": [ "id", "rec", "rec.s", "ae", "ae.s", "recae", "recae.s", "rel", "rel.s", "srv", "srv.s", "year", "agecl", "proph", "match", "dtcens", "dtcens_s" ], "rows": 2279, "table": true, "tojson": true }, { "name": "ebmtcal_cmprsk", "title": "European Group for Blood and Marrow Transplantation data (one row per individual)", "object": "ebmtcal_cmprsk", "class": [ "data.frame" ], "fields": [ "id", "rec", "rec.s", "ae", "ae.s", "recae", "recae.s", "rel", "rel.s", "srv", "srv.s", "year", "agecl", "proph", "match", "dtcens", "dtcens_s" ], "rows": 2279, "table": true, "tojson": true }, { "name": "msebmtcal", "title": "European Group for Blood and Marrow Transplantation data in 'msdata' format.", "object": "msebmtcal", "class": [ "msdata", "data.frame" ], "fields": [ "id", "from", "to", "trans", "Tstart", "Tstop", "time", "status" ], "rows": 15512, "table": true, "tojson": true }, { "name": "msebmtcal_cmprsk", "title": "European Group for Blood and Marrow Transplantation data in competing risks format, for transitions out of the initial state only", "object": "msebmtcal_cmprsk", "class": [ "msdata", "data.frame" ], "fields": [ "id", "from", "to", "trans", "Tstart", "Tstop", "time", "status" ], "rows": 9116, "table": true, "tojson": true }, { "name": "tp_cmprsk_j0", "title": "Predicted risks for a competing risks model out of state j = 0", "object": "tp_cmprsk_j0", "class": [ "data.frame" ], "fields": [ "id", "pstate1", "pstate2", "pstate3", "pstate4", "pstate5", "pstate6", "se1", "se2", "se3", "se4", "se5", "se6" ], "rows": 2279, "table": true, "tojson": true }, { "name": "tps0", "title": "Predicted transition probabilities out of transplant state made at time s = 0", "object": "tps0", "class": [ "data.frame" ], "fields": [ "id", "pstate1", "pstate2", "pstate3", "pstate4", "pstate5", "pstate6", "se1", "se2", "se3", "se4", "se5", "se6", "j" ], "rows": 2279, "table": true, "tojson": true }, { "name": "tps100", "title": "Predicted transition probabilities out of every state made at time s = 100", "object": "tps100", "class": [ "data.frame" ], "fields": [ "id", "pstate1", "pstate2", "pstate3", "pstate4", "pstate5", "pstate6", "se1", "se2", "se3", "se4", "se5", "se6", "j" ], "rows": 13674, "table": true, "tojson": true } ], "_help": [ { "page": "calc_weights", "title": "Calculate inverse probability of censoring weights at time 't'.", "topics": [ "calc_weights" ] }, { "page": "calib_msm", "title": "Assess the calibration of a multistate model", "topics": [ "calib_msm" ] }, { "page": "ebmtcal", "title": "European Group for Blood and Marrow Transplantation data (one row per individual)", "topics": [ "ebmtcal" ] }, { "page": "ebmtcal_cmprsk", "title": "European Group for Blood and Marrow Transplantation data (one row per individual)", "topics": [ "ebmtcal_cmprsk" ] }, { "page": "metadata", "title": "Create S3 generic for printing metadata", "topics": [ "metadata" ] }, { "page": "msebmtcal", "title": "European Group for Blood and Marrow Transplantation data in 'msdata' format.", "topics": [ "msebmtcal" ] }, { "page": "msebmtcal_cmprsk", "title": "European Group for Blood and Marrow Transplantation data in competing risks format, for transitions out of the initial state only", "topics": [ "msebmtcal_cmprsk" ] }, { "page": "plot.calib_mlr", "title": "Plots calibration scatter plots for objects of class 'calib_mlr' estimated using using 'calib_msm'.", "topics": [ "plot.calib_mlr" ] }, { "page": "plot.calib_msm", "title": "Plots calibration curves estimated using 'calib_msm'.", "topics": [ "plot.calib_msm" ] }, { "page": "tp_cmprsk_j0", "title": "Predicted risks for a competing risks model out of state j = 0", "topics": [ "tp_cmprsk_j0" ] }, { "page": "tps0", "title": "Predicted transition probabilities out of transplant state made at time s = 0", "topics": [ "tps0" ] }, { "page": "tps100", "title": "Predicted transition probabilities out of every state made at time s = 100", "topics": [ "tps100" ] } ], "_readme": "https://github.com/alexpate30/calibmsm/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "base64enc", "boot", "broom", "bslib", "cachem", "car", "carData", "checkmate", "cli", "cluster", "codetools", "colorspace", "colourpicker", "commonmark", "corrplot", "cowplot", "cpp11", "data.table", "Deriv", "digest", "doBy", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "forecast", "foreign", "Formula", "fracdiff", "fs", "generics", "ggExtra", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mgcv", "microbenchmark", "mime", "miniUI", "minqa", "modelr", "mstate", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "otel", "pbkrtest", "pillar", "pkgconfig", "polspline", "polynom", "promises", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rmarkdown", "rms", "rpart", "rstatix", "rstudioapi", "S7", "sandwich", "sass", "scales", "shiny", "shinyjs", "sourcetools", "SparseM", "stringi", "stringr", "survival", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "VGAM", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "Directory-of-vignettes.Rmd", "filename": "Directory-of-vignettes.html", "title": "A catalogue of links and descriptions for the vignettes/articles", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-08-26 12:59:22", "modified": "2024-11-04 14:23:10", "commits": 29 }, { "source": "overview_guide.pdf.asis", "filename": "overview_guide.pdf", "title": "A guide on how to use calibmsm", "engine": "R.rsp::asis", "headings": [], "created": "2024-04-24 10:57:56", "modified": "2024-04-24 10:57:56", "commits": 1 } ], "_score": 4.819543935541869, "_indexed": true, "_nocasepkg": "calibmsm", "_universes": [ "alexpate30" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.3", "date": "2026-05-15T09:02:56.000Z", "distro": "noble", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "511ca756971f5f4813121c79cd16e08f6fd06f5f7f0ef16b8e560921c980d98e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.6.0", "os": "linux", "version": "1.1.3", "date": "2026-05-15T09:03:31.000Z", "distro": "noble", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "33b10a7b9dadb72a490da73f5970397932505e84efce484e27e9e65c7a0dde5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.5.3", "os": "mac", "version": "1.1.3", "date": "2026-05-15T09:02:11.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "ec1c6100ecabcf02f1668153c6dffd96cd2f08480d53d1451758de663bdd24fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.6.0", "os": "mac", "version": "1.1.3", "date": "2026-05-15T09:02:23.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "cc7d7e2bc9ddaae55f9c0ba3d98fa0f80342adb62e1fbca956385badbc52dc14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.7.0", "os": "win", "version": "1.1.3", "date": "2026-05-15T09:01:36.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "2976ed95d1d15c7207ef7e4c2218b409ce75afbcd5e4f112e8e33ba6adcaeb37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.5.3", "os": "win", "version": "1.1.3", "date": "2026-05-15T09:01:37.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "68c3d17e33fb2a89617cc94ecebc12839b20f3640c03fa1a018a7c23ef725aff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.6.0", "os": "win", "version": "1.1.3", "date": "2026-05-15T09:01:26.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "4dd6a57456c4ef5eb906e7ea03847c99b27aa3ff0d08be1630eb916e51be4b9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.3", "date": "2026-06-02T19:33:01.000Z", "commit": "487de8d602609713628bea868f04c06f77896daa", "fileid": "9d5bcdf909a55d516027550fc9c5608634769c3a3c5fba18e2ec4a0df17dc326", "status": "success", "buildurl": "https://github.com/r-universe/alexpate30/actions/runs/25909279835" } ] }