{ "_id": "6a646981059529545f5774a3", "Package": "etm", "Type": "Package", "Title": "Empirical Transition Matrix", "Version": "1.1.2", "Authors@R": "c(person(\"Arthur\", \"Allignol\", role = \"aut\",\nemail = \"arthur.allignol@gmail.com\"),\nperson(\"Mark\", \"Clements\", role = c(\"cre\",\"aut\"),\nemail = \"mark.clements@ki.se\"))", "Description": "The etm (empirical transition matrix) package permits to\nestimate the matrix of transition probabilities for any\ntime-inhomogeneous multi-state model with finite state space\nusing the Aalen-Johansen estimator. Functions for data\npreparation and for displaying are also included (Allignol et\nal., 2011 ). Functionals of the\nAalen-Johansen estimator, e.g., excess length-of-stay in an\nintermediate state, can also be computed (Allignol et al. 2011\n).", "License": "MIT + file LICENSE", "NeedsCompilation": "yes", "Repository": "https://mclements.r-universe.dev", "Date/Publication": "2025-04-12 08:09:43 UTC", "RemoteUrl": "https://github.com/mclements/etm", "RemoteRef": "HEAD", "RemoteSha": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "Packaged": { "Date": "2026-07-25 07:37:18 UTC", "User": "root" }, "Author": "Arthur Allignol [aut],\nMark Clements [cre, aut]", "Maintainer": "Mark Clements ", "_user": "mclements", "_type": "src", "_file": "etm_1.1.2.tar.gz", "_fileid": "https://r2.ropensci.org/8d3c01a32204c94acef0bc8a84888b0bc735a7fdcab9129f735bbe6d75ac0460", "_filesize": 392469, "_sha256": "8d3c01a32204c94acef0bc8a84888b0bc735a7fdcab9129f735bbe6d75ac0460", "_expires": "2026-11-02T07:45:02.000Z", "_created": "2026-07-25T07:37:18.000Z", "_published": "2026-07-25T07:45:05.417Z", "_jobs": [ { "job": 89657697817, "time": 142, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8617219285" }, { "job": 89657697812, "time": 184, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8617226292" }, { "job": 89657697813, "time": 142, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8617219278" }, { "job": 89657697824, "time": 174, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8617224613" }, { "job": 89657697815, "time": 135, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8617224323" }, { "job": 89657697807, "time": 333, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8617263603" }, { "job": 89657697825, "time": 112, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8617226708" }, { "job": 89657697805, "time": 296, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8617252559" }, { "job": 89657392804, "time": 234, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8617196037" }, { "job": 89657697809, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8617215723" }, { "job": 89657697801, "time": 150, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8617220587" }, { "job": 89657697816, "time": 160, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8617222312" }, { "job": 89657697823, "time": 164, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8617222739" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183", "_status": "success", "_upstream": "https://github.com/mclements/etm", "_commit": { "id": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "author": "Mark Clements ", "committer": "Mark Clements ", "message": "Rename clos.X to clos_X for non-exported functions\n\nThis includes clos.nocp, clos.cp, clos.cp_pure and clos.nocp_pure\n\nAs a TODO, we could export and document the pure functions.\n", "time": 1744445383 }, "_maintainer": { "name": "Mark Clements", "email": "mark.clements@ki.se", "login": "mclements", "description": "", "uuid": 557321 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "survival", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.11.4", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "kmi", "role": "Suggests" }, { "package": "geepack", "role": "Suggests" } ], "_owner": "mclements", "_selfowned": true, "_usedby": 16, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "mclements", "count": 24, "uuid": 557321 }, { "user": "aallignol", "count": 1, "uuid": 11571187 } ], "_userbio": { "uuid": 557321, "type": "user", "name": "mclements", "followers": 66 }, "_downloads": { "count": 7525, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/etm" }, "_mentions": 17, "_devurl": "https://github.com/mclements/etm", "_searchresults": 128, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/etm.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/mclements/etm", "_realowner": "mclements", "_cranurl": true, "_releases": [ { "version": "0.3-2", "date": "2008-07-15" }, { "version": "0.3-3", "date": "2008-10-30" }, { "version": "0.3-5", "date": "2008-12-18" }, { "version": "0.3-6", "date": "2009-02-01" }, { "version": "0.3-7", "date": "2009-02-04" }, { "version": "0.4-0", "date": "2009-04-14" }, { "version": "0.4-3", "date": "2009-06-14" }, { "version": "0.4-6", "date": "2009-09-03" }, { "version": "0.4-7", "date": "2009-11-12" }, { "version": "0.5", "date": "2010-11-04" }, { "version": "0.5-1", "date": "2010-11-29" }, { "version": "0.5-2", "date": "2011-01-03" }, { "version": "0.5-4", "date": "2012-04-04" }, { "version": "0.6", "date": "2013-12-18" }, { "version": "0.6-1", "date": "2014-03-27" }, { "version": "0.6-2", "date": "2014-12-09" }, { "version": "0.6-2.1", "date": "2018-06-11" }, { "version": "1.0.3", "date": "2018-07-04" }, { "version": "1.0.4", "date": "2018-07-11" }, { "version": "1.0.5", "date": "2019-05-28" }, { "version": "1.0.5.1", "date": "2020-01-29" }, { "version": "1.1", "date": "2020-04-20" }, { "version": "1.1.1", "date": "2020-09-08" }, { "version": "1.1.2", "date": "2025-04-12" } ], "_exports": [ "clos", "closPseudo", "etm", "etmCIF", "etmprep", "prepare.los.data", "tra_comp", "tra_ill", "tra_ill_comp", "tra_surv", "trcov", "trprob" ], "_datasets": [ { "name": "abortion", "title": "Pregnancies exposed to coumarin derivatives", "object": "abortion", "file": "abortion.txt.gz", "class": [ "data.frame" ], "fields": [ "id", "entry", "exit", "group", "cause" ], "rows": 1186, "table": true, "tojson": true }, { "name": "fourD", "title": "Placebo data from the 4D study", "object": "fourD", "file": "fourD.rda", "class": [ "data.frame" ], "fields": [ "id", "sex", "age", "medication", "status", "time", "treated" ], "rows": 636, "table": true, "tojson": true }, { "name": "los.data", "title": "Length of hospital stay", "object": "los.data", "file": "los.data.csv.gz", "class": [ "data.frame" ], "fields": [ "adm.id", "j.01", "j.02", "j.03", "j.12", "j.13", "cens" ], "rows": 756, "table": true, "tojson": true }, { "name": "sir.cont", "title": "Ventilation status in intensive care unit patients", "object": "sir.cont", "file": "sir.cont.txt.gz", "class": [ "data.frame" ], "fields": [ "id", "from", "to", "time", "age", "sex" ], "rows": 1141, "table": true, "tojson": true } ], "_help": [ { "page": "abortion", "title": "Pregnancies exposed to coumarin derivatives", "topics": [ "abortion" ] }, { "page": "clos", "title": "Change in Length of Stay", "topics": [ "clos", "clos.etm", "clos.msfit" ] }, { "page": "closPseudo", "title": "Pseudo Value Regression for the Extra Length-of-Stay", "topics": [ "closPseudo" ] }, { "page": "etm", "title": "Computation of the empirical transition matrix", "topics": [ "etm", "etm.data.frame" ] }, { "page": "etmCIF", "title": "Cumulative incidence functions of competing risks", "topics": [ "etmCIF" ] }, { "page": "etmprep", "title": "Data transformation function for using etm", "topics": [ "etmprep" ] }, { "page": "fourD", "title": "Placebo data from the 4D study", "topics": [ "fourD" ] }, { "page": "lines.etm", "title": "Lines method for 'etm' objects", "topics": [ "lines.etm" ] }, { "page": "los.data", "title": "Length of hospital stay", "topics": [ "los.data" ] }, { "page": "plot.clos.etm", "title": "Plot method for 'clos.etm' objects", "topics": [ "plot.clos.etm" ] }, { "page": "plot.etm", "title": "Plot method for an etm object", "topics": [ "plot.etm" ] }, { "page": "plot.etmCIF", "title": "Plot cumulative incidence functions", "topics": [ "plot.etmCIF" ] }, { "page": "prepare.los.data", "title": "Prepare the data for clos", "topics": [ "prepare.los.data" ] }, { "page": "print.clos.etm", "title": "Print function for 'clos.etm' objects", "topics": [ "print.clos.etm" ] }, { "page": "print.etm", "title": "Print method for object of class 'etm'", "topics": [ "print.etm" ] }, { "page": "print.etmCIF", "title": "Print function for 'cifETM' objects", "topics": [ "print.etmCIF" ] }, { "page": "sir.cont", "title": "Ventilation status in intensive care unit patients", "topics": [ "sir.cont" ] }, { "page": "summary.etm", "title": "Summary methods for an 'etm' object", "topics": [ "print.summary.etm", "summary.etm" ] }, { "page": "summary.etmCIF", "title": "Summary function for cifETM", "topics": [ "print.summary.etmCIF", "summary.etmCIF" ] }, { "page": "tra", "title": "Matrix of possible transitions", "topics": [ "tra", "tra_comp", "tra_ill", "tra_ill_comp", "tra_surv" ] }, { "page": "trprob_trcov", "title": "Function to extract transition probabilities and (co)variance", "topics": [ "trcov", "trcov.etm", "trprob", "trprob.etm" ] }, { "page": "xyplot.etm", "title": "xyplot method for object of class 'etm'", "topics": [ "xyplot.etm" ] } ], "_readme": "https://github.com/mclements/etm/raw/HEAD/README.md", "_rundeps": [ "data.table", "lattice", "Matrix", "Rcpp", "RcppArmadillo", "survival" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "etmCIF_tutorial.Rnw", "filename": "etmCIF_tutorial.pdf", "title": "Computing Cumulative Incidence Functions with the etmCIF Function", "engine": "utils::Sweave", "headings": [], "created": "2020-09-02 15:20:18", "modified": "2020-09-02 15:20:18", "commits": 1 } ], "_score": 8.363927715625355, "_indexed": true, "_nocasepkg": "etm", "_universes": [ "mclements" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-07-25T07:39:27.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/5e6cf0fed8bbccb794baf3c13ae7c0c68e192fa4fc0f32caa8a1e950fdf1a5d2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-07-25T07:39:51.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/ccb85dde1c79ebb54899b8fb31fbf7a07e0eee98865acf5f5ebf0e9ae3bc447c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.1", "os": "linux", "version": "1.1.2", "date": "2026-07-25T07:39:27.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/d01c9b3b70a1df6c0f721d9adf1da27425dbbe683c15b4e9c7259fefacf5528d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.1", "os": "linux", "version": "1.1.2", "date": "2026-07-25T07:39:48.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/24175d42dfbba78eb7af5768446d0c272e4de4ea676403c05b1c77b8e061ebb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.5.3", "os": "mac", "version": "1.1.2", "date": "2026-07-25T07:40:02.000Z", "arch": "aarch64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/728b3f30d95827d5edff23780db85b0d0ade40dfa8368851e2b99eed95912917", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.5.3", "os": "mac", "version": "1.1.2", "date": "2026-07-25T07:42:47.000Z", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/14783dfe57bc01842a76598445e4191ee9cb54b802a69a0076eac9e788b1f606", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.1", "os": "mac", "version": "1.1.2", "date": "2026-07-25T07:40:20.000Z", "arch": "aarch64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/9751513eed83e43e03dd372ca4a2831245a4f8021f33645dff7e3f7f85f9b64f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.1", "os": "mac", "version": "1.1.2", "date": "2026-07-25T07:41:28.000Z", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/64cc6f85e38853dc6ff96f2ed3a8b52150bfaa23044744a67a108fd9adcb83d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.2", "date": "2026-07-25T07:39:39.000Z", "arch": "emscripten", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/6761ea3dc85f98c8a8b97e2fa5b10e1cb7b075fc2d97d64187bbb0b57654f166", "status": "success", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.7.0", "os": "win", "version": "1.1.2", "date": "2026-07-25T07:38:46.000Z", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/9656083642444a6167fc4c039ab397792b769ace24d6edbe54079da4fc982bb7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.5.3", "os": "win", "version": "1.1.2", "date": "2026-07-25T07:38:46.000Z", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/f320ae4c7a4b6e2d53b2e106af38b1a037f432f6bd37dda52497058782518c21", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" }, { "r": "4.6.1", "os": "win", "version": "1.1.2", "date": "2026-07-25T07:38:51.000Z", "arch": "x86_64", "commit": "f9ff9b45524e83ac79f3c5db6170f6d724a328a5", "fileid": "https://r2.ropensci.org/b3a4303d404e65034ff703affd01b65f2941278c3c59e00ee194d6040bea1bbe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mclements/actions/runs/30149526183" } ] }