{ "_id": "6a1e9e551d7bb097a0a6fc4e", "Package": "pmrm", "Title": "Progression Models for Repeated Measures", "Description": "A progression model for repeated measures (PMRM) is a\ncontinuous-time nonlinear mixed-effects model for longitudinal\nclinical trials in progressive diseases. Unlike mixed models\nfor repeated measures (MMRMs), which estimate treatment effects\nas linear combinations of additive effects on the outcome\nscale, PMRMs characterize treatment effects in terms of the\nunderlying disease trajectory. This framing yields clinically\ninterpretable quantities such as average time saved and percent\nreduction in decline due to treatment. This package implements\nfrequentist PMRMs by Raket (2022) using\n'RTMB' by Kristensen (2016) .", "Version": "0.0.4.9000", "License": "MIT + file LICENSE", "URL": "https://github.com/openpharma/pmrm,\nhttps://openpharma.github.io/pmrm/", "BugReports": "https://github.com/openpharma/pmrm/issues", "Authors@R": "c(\nperson(\ngiven = c(\"William\", \"Michael\"),\nfamily = \"Landau\",\nemail = \"will.landau.oss@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1878-3253\"),\nrole = c(\"aut\", \"cre\")\n),\nperson(\ngiven = c(\"Lars\", \"Lau\"),\nfamily = \"Raket\",\nemail = \"larslau.raket@lilly.com\",\ncomment = c(ORCID = \"0000-0001-7099-2314\"),\nrole = \"aut\"\n),\nperson(\ngiven = \"Kasper\",\nfamily = \"Kristensen\",\nrole = \"aut\",\nemail = \"kaskr@dtu.dk\",\ncomment = c(ORCID=\"0000-0003-3425-3762\")\n),\nperson(\nfamily = \"Eli Lilly and Company\",\nrole = c(\"cph\", \"fnd\")\n))", "Encoding": "UTF-8", "Language": "en-US", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Repository": "https://openpharma.r-universe.dev", "Date/Publication": "2026-04-03 20:26:51 UTC", "RemoteUrl": "https://github.com/openpharma/pmrm", "RemoteRef": "HEAD", "RemoteSha": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 09:06:50 UTC", "User": "root" }, "Author": "William Michael Landau [aut, cre] (ORCID:\n),\nLars Lau Raket [aut] (ORCID: ),\nKasper Kristensen [aut] (ORCID:\n),\nEli Lilly and Company [cph, fnd]", "Maintainer": "William Michael Landau ", "MD5sum": "1091b9368748b600bcbec55453402ed8", "_user": "openpharma", "_type": "src", "_file": "pmrm_0.0.4.9000.tar.gz", "_fileid": "4114c2e8818376b47c3891c1a1a5ed17f74d8dac2de23864e774fc73594b2c72", "_filesize": 1986422, "_sha256": "4114c2e8818376b47c3891c1a1a5ed17f74d8dac2de23864e774fc73594b2c72", "_created": "2026-06-02T09:06:50.000Z", "_published": "2026-06-02T09:11:49.395Z", "_distro": "noble", "_jobs": [ { "job": 79036933224, "time": 227, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7353591994" }, { "job": 79036933242, "time": 223, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7353590236" }, { "job": 79036933194, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7353586210" }, { "job": 79036933358, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7353565640" }, { "job": 79035992088, "time": 328, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7353510313" }, { "job": 79036933147, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353553889" }, { "job": 79036933261, "time": 164, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7353570077" }, { "job": 79036933442, "time": 153, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7353566717" }, { "job": 79036933288, "time": 169, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7353571732" } ], "_buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/openpharma/pmrm", "_commit": { "id": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "author": "wlandau ", "committer": "wlandau ", "message": "dev version\n", "time": 1775248011 }, "_maintainer": { "name": "William Michael Landau", "email": "will.landau.oss@gmail.com", "login": "wlandau", "orcid": "0000-0003-1878-3253", "twitter": "@wmlandau", "description": "Statistician and developer", "uuid": 1580860 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "generics", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "nlme", "role": "Imports" }, { "package": "RTMB", "version": ">= 1.8", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "openpharma", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 44 }, { "week": "2026-05", "n": 6 }, { "week": "2026-06", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-09", "n": 4 }, { "week": "2026-11", "n": 2 }, { "week": "2026-14", "n": 9 } ], "_tags": [ { "name": "0.0.1", "date": "2026-01-23" }, { "name": "0.0.2", "date": "2026-01-26" }, { "name": "0.0.3", "date": "2026-03-12" }, { "name": "0.0.4", "date": "2026-04-03" } ], "_topics": [ "adcomp", "disease-progression-model", "mmrm", "pmrm", "rtmb", "tmb" ], "_stars": 6, "_contributors": [ { "user": "wlandau", "count": 69, "uuid": 1580860 } ], "_userbio": { "uuid": 8436743, "type": "organization", "name": "openpharma", "description": "Further precompetitive collaboration in life sciences" }, "_downloads": { "count": 507, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pmrm" }, "_devurl": "https://github.com/openpharma/pmrm", "_pkgdown": "https://openpharma.github.io/pmrm/", "_searchresults": 2, "_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/pmrm.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/openpharma/pmrm", "_realowner": "openpharma", "_cranurl": true, "_releases": [ { "version": "0.0.2", "date": "2026-01-30" }, { "version": "0.0.3", "date": "2026-03-12" }, { "version": "0.0.4", "date": "2026-04-03" } ], "_exports": [ "AIC", "BIC", "confint", "deviance", "fitted", "glance", "logLik", "pmrm_estimates", "pmrm_marginals", "pmrm_model_decline_nonproportional", "pmrm_model_decline_proportional", "pmrm_model_slowing_nonproportional", "pmrm_model_slowing_proportional", "pmrm_simulate_decline_nonproportional", "pmrm_simulate_decline_proportional", "pmrm_simulate_slowing_nonproportional", "pmrm_simulate_slowing_proportional", "predict", "residuals", "tidy", "VarCorr" ], "_help": [ { "page": "AIC.pmrm_fit", "title": "Akaike information criterion (AIC)", "concept": [ "model comparison" ], "topics": [ "AIC.pmrm_fit" ] }, { "page": "BIC.pmrm_fit", "title": "Bayesian information criterion (BIC)", "concept": [ "model comparison" ], "topics": [ "BIC.pmrm_fit" ] }, { "page": "coef.pmrm_fit", "title": "Treatment effect parameters", "concept": [ "estimates" ], "topics": [ "coef.pmrm_fit" ] }, { "page": "confint.pmrm_fit", "title": "Confidence intervals of parameters", "concept": [ "model comparison" ], "topics": [ "confint.pmrm_fit" ] }, { "page": "deviance.pmrm_fit", "title": "Deviance", "concept": [ "model comparison" ], "topics": [ "deviance.pmrm_fit" ] }, { "page": "fitted.pmrm_fit", "title": "Fitted values", "concept": [ "predictions" ], "topics": [ "fitted.pmrm_fit" ] }, { "page": "glance.pmrm_fit", "title": "Glance at a PMRM.", "concept": [ "model comparison" ], "topics": [ "glance.pmrm_fit" ] }, { "page": "logLik.pmrm_fit", "title": "Extract the log likelihood.", "concept": [ "model comparison" ], "topics": [ "logLik.pmrm_fit" ] }, { "page": "plot.pmrm_fit", "title": "Plot a fitted PMRM.", "concept": [ "visualization" ], "topics": [ "plot.pmrm_fit" ] }, { "page": "pmrm_estimates", "title": "Parameter estimates and confidence intervals", "concept": [ "estimates and predictions" ], "topics": [ "pmrm_estimates" ] }, { "page": "pmrm_marginals", "title": "Marginal means", "concept": [ "estimates" ], "topics": [ "pmrm_marginals" ] }, { "page": "pmrm_model_decline_nonproportional", "title": "Fit the non-proportional decline model.", "concept": [ "models" ], "topics": [ "pmrm_model_decline_nonproportional" ] }, { "page": "pmrm_model_decline_proportional", "title": "Fit the proportional decline model.", "concept": [ "models" ], "topics": [ "pmrm_model_decline_proportional" ] }, { "page": "pmrm_model_slowing_nonproportional", "title": "Fit the non-proportional slowing model.", "concept": [ "models" ], "topics": [ "pmrm_model_slowing_nonproportional" ] }, { "page": "pmrm_model_slowing_proportional", "title": "Fit the proportional slowing model.", "concept": [ "models" ], "topics": [ "pmrm_model_slowing_proportional" ] }, { "page": "pmrm_simulate_decline_nonproportional", "title": "Simulate non-proportional decline model.", "concept": [ "simulations" ], "topics": [ "pmrm_simulate_decline_nonproportional" ] }, { "page": "pmrm_simulate_decline_proportional", "title": "Simulate proportional decline model.", "concept": [ "simulations" ], "topics": [ "pmrm_simulate_decline_proportional" ] }, { "page": "pmrm_simulate_slowing_nonproportional", "title": "Simulate non-proportional slowing model.", "concept": [ "simulations" ], "topics": [ "pmrm_simulate_slowing_nonproportional" ] }, { "page": "pmrm_simulate_slowing_proportional", "title": "Simulate proportional slowing model.", "concept": [ "simulations" ], "topics": [ "pmrm_simulate_slowing_proportional" ] }, { "page": "predict.pmrm_fit", "title": "Predict new outcomes", "concept": [ "predictions" ], "topics": [ "predict.pmrm_fit" ] }, { "page": "print.pmrm_fit", "title": "Print a fitted PMRM.", "concept": [ "visualization" ], "topics": [ "print.pmrm_fit" ] }, { "page": "residuals.pmrm_fit", "title": "'pmrm' residuals.", "concept": [ "predictions" ], "topics": [ "residuals.pmrm_fit" ] }, { "page": "summary.pmrm_fit", "title": "Summarize a PMRM.", "concept": [ "model comparison" ], "topics": [ "summary.pmrm_fit" ] }, { "page": "tidy.pmrm_fit", "title": "Tidy a fitted PMRM.", "concept": [ "estimates" ], "topics": [ "tidy.pmrm_fit" ] }, { "page": "VarCorr.pmrm_fit", "title": "Estimated covariance matrix", "concept": [ "estimates" ], "topics": [ "VarCorr.pmrm_fit" ] }, { "page": "vcov.pmrm_fit", "title": "Treatment effect parameter covariance matrix", "concept": [ "estimates" ], "topics": [ "vcov.pmrm_fit" ] } ], "_pkglogo": "https://github.com/openpharma/pmrm/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/openpharma/pmrm/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "nlme", "pillar", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "RTMB", "S7", "scales", "tibble", "tidyselect", "TMB", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "models.Rmd", "filename": "models.html", "title": "Models", "engine": "knitr::rmarkdown", "headings": [ "Common elements", "Data", "Likelihood", "Variance", "Expected value of the control group", "The decline models", "The non-proportional decline model", "The proportional decline model", "The slowing models", "The non-proportional slowing model", "The proportional slowing model", "References" ], "created": "2026-01-20 13:49:33", "modified": "2026-01-21 15:46:49", "commits": 8 }, { "source": "usage.Rmd", "filename": "usage.html", "title": "Usage", "engine": "knitr::rmarkdown", "headings": [ "Raw data", "Models", "Checking and troubleshooting", "Summaries", "Marginals", "Predictions", "Plots" ], "created": "2026-01-20 13:49:33", "modified": "2026-01-22 21:35:01", "commits": 3 }, { "source": "validation.Rmd", "filename": "validation.html", "title": "Validation", "engine": "knitr::rmarkdown", "headings": [ "Implementation", "Last run", "Convergence", "Parameter coverage" ], "created": "2026-01-23 20:46:55", "modified": "2026-01-23 21:16:38", "commits": 2 } ], "_score": 5.799340549453581, "_indexed": true, "_nocasepkg": "pmrm", "_universes": [ "openpharma", "wlandau" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.4.9000", "date": "2026-06-02T09:09:28.000Z", "distro": "noble", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "1f05cf487485fef015a1cb1667e00dd680843d9fb1fd52e662138af98877580a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.6.0", "os": "linux", "version": "0.0.4.9000", "date": "2026-06-02T09:09:23.000Z", "distro": "noble", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "ed0f59c8ecb7469e2def42b63ab16e51e20ffed6480c39d28ef79eddd1cfa0c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.5.3", "os": "mac", "version": "0.0.4.9000", "date": "2026-06-02T09:09:16.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "307288800bd7eb8ce2fe945095c36d106e5a973dbd86f041eb6b43ddfc1e7c37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.6.0", "os": "mac", "version": "0.0.4.9000", "date": "2026-06-02T09:08:52.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "b373ec0040608fb2701244e1944ce263193300b4d45838d6bcf58eaa5b6ffa14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.4.9000", "date": "2026-06-02T09:09:16.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "11a0405b00e974e198b43c9b5662fa286afdf85283a432ff8d5f2b4f7a8154ff", "status": "success", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.7.0", "os": "win", "version": "0.0.4.9000", "date": "2026-06-02T09:08:16.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "549ac5f0480bd68e707a489ee2c7eba36f0aa41c7ce08f73f016ba8b76ac408a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.5.3", "os": "win", "version": "0.0.4.9000", "date": "2026-06-02T09:08:23.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "82a1f2817d40d1dedc513246a93d2868b07278b31aef3e35fb1ac6d863d25ab5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" }, { "r": "4.6.0", "os": "win", "version": "0.0.4.9000", "date": "2026-06-02T09:08:26.000Z", "commit": "05b3fd1307dd4fd9693112be2d7ce00e2b1e148f", "fileid": "7c85203bfd214335c39cd2fc3c983c412471e3ea2c8d09c7198b38b9dbf93316", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openpharma/actions/runs/26809552221" } ] }