{ "_id": "6a1041e7acfb0bcc41c9d9b7", "Package": "presmoothedTP", "Type": "Package", "Title": "Presmoothed Landmark Aalen-Johansen Estimator of Transition\nProbabilities for Complex Multi-State Models", "Version": "0.1.0", "Authors@R": "c(\nperson(\ngiven = \"Gustavo\",\nfamily = \"Soutinho\",\nrole = c(\"aut\", \"cre\"),\nemail = \"gustavosoutinho@sapo.pt\",\ncomment = c(ORCID = \"0000-0002-0559-1327\")\n),\nperson(\ngiven = \"Luis\",\nfamily = \"Meira-Machado\",\nrole = \"aut\",\nemail = \"lmachado@math.uminho.pt\",\ncomment = c(ORCID = \"0000-0002-8577-7665\")\n)\n)", "Description": "Multi-state models are essential tools in longitudinal\ndata analysis. One primary goal of these models is the\nestimation of transition probabilities, a critical metric for\npredicting clinical prognosis across various stages of diseases\nor medical conditions. Traditionally, inference in multi-state\nmodels relies on the Aalen-Johansen (AJ) estimator which is\nconsistent under the Markov assumption. However, in many\npractical applications, the Markovian nature of the process is\noften not guaranteed, limiting the applicability of the AJ\nestimator in more complex scenarios. This package extends the\nlandmark Aalen-Johansen estimator (Putter, H, Spitoni, C (2018)\n) incorporating presmoothing\ntechniques described by Soutinho, Meira-Machado and Oliveira\n(2020) , offering a robust\nalternative for estimating transition probabilities in\nnon-Markovian multi-state models with multiple states and\npotential reversible transitions.", "License": "GPL-3", "RoxygenNote": "7.3.1", "Encoding": "UTF-8", "LazyLoad": "yes", "LazyData": "yes", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-11 07:32:34 UTC", "User": "root" }, "Author": "Gustavo Soutinho [aut, cre]\n(), Luis Meira-Machado\n[aut] ()", "Maintainer": "Gustavo Soutinho ", "Repository": "https://gsoutinho.r-universe.dev", "Date/Publication": "2025-01-22 17:10:02 UTC", "RemoteUrl": "https://github.com/cran/presmoothedTP", "RemoteRef": "HEAD", "RemoteSha": "bf85b263948f42d3ad076b889e4c022a190d091f", "MD5sum": "f429c239905da94f2ffda255a2a5324f", "_user": "gsoutinho", "_type": "src", "_file": "presmoothedTP_0.1.0.tar.gz", "_fileid": "0f817a5097757cce5bf86df8360c10a6ebf5519e992aafffc779049e3ed0f76d", "_filesize": 201517, "_sha256": "0f817a5097757cce5bf86df8360c10a6ebf5519e992aafffc779049e3ed0f76d", "_created": "2026-05-11T07:32:34.000Z", "_published": "2026-05-22T11:45:43.926Z", "_distro": "noble", "_jobs": [ { "job": 77373058795, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6912722888" }, { "job": 77373058616, "time": 122, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6912722093" }, { "job": 77373058518, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6912718893" }, { "job": 77373058749, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6912725200" }, { "job": 77373058451, "time": 157, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6912683900" }, { "job": 77373058193, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159701628" }, { "job": 77373058867, "time": 98, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6912714565" }, { "job": 77373058743, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6912711588" }, { "job": 77373058829, "time": 90, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6912712217" } ], "_buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/presmoothedTP", "_commit": { "id": "bf85b263948f42d3ad076b889e4c022a190d091f", "author": "Gustavo Soutinho ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1737565802 }, "_maintainer": { "name": "Gustavo Soutinho", "email": "gustavosoutinho@sapo.pt", "login": "gsoutinho", "uuid": 2633897, "orcid": "0000-0002-0559-1327" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "survival", "role": "Imports" }, { "package": "mstate", "role": "Imports" }, { "package": "plyr", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "gsoutinho", "count": 1, "uuid": 2633897 } ], "_userbio": { "uuid": 2633897, "type": "user", "name": "gsoutinho" }, "_downloads": { "count": 171, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/presmoothedTP" }, "_searchresults": 0, "_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/presmoothedTP.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "gsoutinho", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2025-01-22" } ], "_exports": [ "prepTP", "presmoothTP", "transTP", "unsmoothTP" ], "_datasets": [ { "name": "colonMSM", "title": "Chemotherapy for Stage B/C colon cancer.", "object": "colonMSM", "class": [ "data.frame" ], "fields": [ "time1", "event1", "Stime", "event", "rx", "sex", "age", "obstruct", "perfor", "adhere", "nodes", "differ", "extent", "surg", "node4" ], "rows": 929, "table": true, "tojson": true }, { "name": "data", "title": "data", "object": "data", "class": [ "data.frame" ], "fields": [ "y1", "state1", "y2", "state2", "y3", "state3" ], "rows": 500, "table": true, "tojson": true }, { "name": "ebmt4", "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT).", "object": "ebmt4", "class": [ "data.frame" ], "fields": [ "id", "rec", "rec.s", "ae", "ae.s", "recae", "recae.s", "rel", "rel.s", "srv", "srv.s", "year", "agecl", "proph", "match" ], "rows": 2279, "table": true, "tojson": true }, { "name": "prothr", "title": "Liver cirrhosis data - Abnormal prothrombin levels in liver cirrhosis.", "object": "prothr", "class": [ "msdata", "data.frame" ], "fields": [ "id", "from", "to", "trans", "Tstart", "Tstop", "status", "treat" ], "rows": 2152, "table": true, "tojson": true } ], "_help": [ { "page": "colonMSM", "title": "Chemotherapy for Stage B/C colon cancer.", "topics": [ "colonMSM" ] }, { "page": "data", "title": "data", "topics": [ "data" ] }, { "page": "ebmt4", "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT).", "topics": [ "ebmt4" ] }, { "page": "prepTP", "title": "Function to prepare data set for multi-state modeling in long format from data set in wide format.", "topics": [ "prepTP" ] }, { "page": "presmoothTP", "title": "This function implements presmoothed estimates based on the landmark Aalen-Johansen method for non-parametric estimation of transition probabilities in non-Markov multi-state models.", "topics": [ "presmoothTP" ] }, { "page": "prothr", "title": "Liver cirrhosis data - Abnormal prothrombin levels in liver cirrhosis.", "topics": [ "prothr" ] }, { "page": "transTP", "title": "Define transition matrix for multi-state model.", "topics": [ "transTP" ] }, { "page": "unsmoothTP", "title": "This function implements unsmoothed estimates of from the Aalen-Johansen estimator (AJ) and landmark Aalen-Johansen method of Putter & Spitoni (2016) for non-parametric estimation of transition probabilities in non-Markov multi-state models.", "topics": [ "unsmoothTP" ] } ], "_readme": "https://github.com/cran/presmoothedTP/raw/HEAD/README.md", "_rundeps": [ "data.table", "lattice", "Matrix", "mstate", "plyr", "RColorBrewer", "Rcpp", "rlang", "survival", "viridisLite" ], "_score": 1.6989700043360187, "_indexed": true, "_nocasepkg": "presmoothedtp", "_universes": [ "gsoutinho" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-05-11T07:34:22.000Z", "distro": "noble", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "fd943ebdba8f015c6df1fb744195c9cf8c0ce4fc5360162e2a1277eab384af9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-05-11T07:34:20.000Z", "distro": "noble", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "88d8d2c526507736d1d5c0daa8760f7745e214d9b4fd2be77eb8c3d3dbeb2a35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-05-11T07:34:13.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "3f904c67f70a61732830dda1cc26d9f0a19c3407031b6445dc8673847d3b6d7f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0", "date": "2026-05-11T07:34:29.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "0f139897b90763f1f159d59a6ecf47f545deb04236bc09515abdbb1c1a27779c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-05-11T07:33:48.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "db04fecaa03fb26af501e947e9161f7cd0f51d9ebaf5167a1b275b864a0f6cf4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-05-11T07:33:41.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "115e98b9a39d25e38ab110ab1cebd1cd1ba3edede903e3c895722a3247d9c8cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.6.0", "os": "win", "version": "0.1.0", "date": "2026-05-11T07:33:41.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "3f239d2c0cd64aa2c2d5ec73e9bb9f2422a79b969c8271903f2465327652939b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-05-22T11:45:30.000Z", "commit": "bf85b263948f42d3ad076b889e4c022a190d091f", "fileid": "3c863bef98fa30fd8c8272734b491b53371742c70f1457d3a9a81c442d7dfe2c", "status": "success", "buildurl": "https://github.com/r-universe/gsoutinho/actions/runs/25656483483" } ] }