{
  "_id": "6a3560ff3efcd9bda43eac28",
  "Package": "TreatmentPatterns",
  "Type": "Package",
  "Title": "Analyzes Real-World Treatment Patterns of a Study Population of\nInterest",
  "Version": "3.1.2",
  "Authors@R": "c(person(\"Aniek\", \"Markus\", , role = c(\"aut\"), comment = c(ORCID = \"0000-0001-5779-4794\")),\nperson(\"Maarten\", \"van Kessel\", email = \"m.l.vankessel@erasmusmc.nl\", role = c(\"cre\"), comment = c(ORCID = \"0009-0006-8832-6030\")))",
  "Maintainer": "Maarten van Kessel <m.l.vankessel@erasmusmc.nl>",
  "Description": "Computes treatment patterns within a given cohort using\nthe Observational Medical Outcomes Partnership (OMOP) common\ndata model (CDM). As described in Markus, Verhamme, Kors, and\nRijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.",
  "URL": "https://github.com/darwin-eu/TreatmentPatterns,\nhttps://darwin-eu-dev.github.io/TreatmentPatterns/",
  "BugReports": "https://github.com/darwin-eu/TreatmentPatterns/issues",
  "Language": "en-US",
  "License": "Apache License (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "Roxygen": "list(markdown = TRUE)",
  "Collate": "'CDMInterface.R' 'TreatmentPatterns-package.R'\n'TreatmentPatternsResults.R' 'attrition.R' 'computePathways.R'\n'constructPathways.R' 'createSankeyDiagram.R'\n'createSunburstPlot.R' 'executeTreatmentPatterns.R' 'export.R'\n'exportPatientLevel.R' 'getResultsDataModelSpecification.R'\n'ggSunburst.R' 'plotEventDuration.R' 'utils.R'",
  "Config/pak/sysreqs": "libicu-dev libssl-dev libx11-dev xz-utils",
  "Repository": "https://darwin-eu.r-universe.dev",
  "Date/Publication": "2026-02-11 08:22:48 UTC",
  "RemoteUrl": "https://github.com/darwin-eu/treatmentpatterns",
  "RemoteRef": "HEAD",
  "RemoteSha": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-19 14:41:03 UTC",
    "User": "root"
  },
  "Author": "Aniek Markus [aut] (ORCID: <https://orcid.org/0000-0001-5779-4794>),\nMaarten van Kessel [cre] (ORCID:\n<https://orcid.org/0009-0006-8832-6030>)",
  "MD5sum": "baeada9d9abe2138560e20974b6a40e0",
  "_user": "darwin-eu",
  "_type": "src",
  "_file": "TreatmentPatterns_3.1.2.tar.gz",
  "_fileid": "206f60009314da4e10616940745687b8ba8019c2758ba49a82a05abf9d73fb2b",
  "_filesize": 2622745,
  "_sha256": "206f60009314da4e10616940745687b8ba8019c2758ba49a82a05abf9d73fb2b",
  "_created": "2026-06-19T14:41:03.000Z",
  "_published": "2026-06-19T15:32:15.873Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82371597440,
      "time": 276,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7752524627"
    },
    {
      "job": 82371597490,
      "time": 212,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7752503909"
    },
    {
      "job": 82371597478,
      "time": 141,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7752481522"
    },
    {
      "job": 82371597436,
      "time": 142,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7752481696"
    },
    {
      "job": 82370660496,
      "time": 342,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7752436160"
    },
    {
      "job": 82371597439,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7752488600"
    },
    {
      "job": 82371597455,
      "time": 3029,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7753421123"
    },
    {
      "job": 82371597465,
      "time": 2786,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7753343222"
    },
    {
      "job": 82371597477,
      "time": 2925,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7753388917"
    }
  ],
  "_buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/darwin-eu/treatmentpatterns",
  "_commit": {
    "id": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
    "author": "mvankessel-EMC <m.vankessel@mi-erasmusmc.nl>",
    "committer": "Maarten van Kessel <112690347+mvankessel-EMC@users.noreply.github.com>",
    "message": "updated var name\n",
    "time": 1770798168
  },
  "_maintainer": {
    "name": "Maarten van Kessel",
    "email": "m.l.vankessel@erasmusmc.nl",
    "login": "mvankessel-emc",
    "description": "R-Programmer at Medial Informatics at the Erasmus MC.",
    "uuid": 112690347
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "dbplyr",
      "role": "Imports"
    },
    {
      "package": "Andromeda",
      "role": "Imports"
    },
    {
      "package": "CDMConnector",
      "version": ">= 2.2.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    },
    {
      "package": "Eunomia",
      "role": "Suggests"
    },
    {
      "package": "DatabaseConnector",
      "version": ">= 7.0.0",
      "role": "Suggests"
    },
    {
      "package": "SqlRender",
      "role": "Suggests"
    },
    {
      "package": "CohortGenerator",
      "role": "Suggests"
    },
    {
      "package": "ResultModelManager",
      "role": "Suggests"
    },
    {
      "package": "webshot2",
      "role": "Suggests"
    },
    {
      "package": "CirceR",
      "role": "Suggests"
    },
    {
      "package": "duckdb",
      "role": "Suggests"
    },
    {
      "package": "DBI",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "sunburstR",
      "role": "Suggests"
    },
    {
      "package": "networkD3",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "htmlwidgets",
      "role": "Suggests"
    },
    {
      "package": "visOmopResults",
      "role": "Suggests"
    },
    {
      "package": "PaRe",
      "role": "Suggests"
    }
  ],
  "_owner": "darwin-eu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 33
    }
  ],
  "_tags": [
    {
      "name": "v3.1.1",
      "date": "2025-08-25"
    },
    {
      "name": "v3.1.2",
      "date": "2026-02-11"
    }
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "mvankessel-emc",
      "count": 1289,
      "uuid": 112690347
    },
    {
      "user": "aniekmarkus",
      "count": 56,
      "uuid": 60397369
    },
    {
      "user": "ginberg",
      "count": 35,
      "uuid": 7089667
    },
    {
      "user": "cebarboza",
      "count": 17,
      "uuid": 113351542
    },
    {
      "user": "bmosseveld",
      "count": 11,
      "uuid": 7286241
    },
    {
      "user": "rossdwilliams",
      "count": 7,
      "uuid": 34747165
    },
    {
      "user": "prijnbeek",
      "count": 6,
      "uuid": 7252105
    },
    {
      "user": "ablack3",
      "count": 4,
      "uuid": 10227522
    },
    {
      "user": "rowanerasmus",
      "count": 1,
      "uuid": 74538318
    }
  ],
  "_userbio": {
    "uuid": 120334168,
    "type": "organization",
    "name": "Darwin EU® Public Code Repository",
    "followers": 59,
    "description": "DARWIN EU® will deliver real-world evidence from across Europe on diseases, populations and the uses and performance of medicines."
  },
  "_downloads": {
    "count": 599,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TreatmentPatterns"
  },
  "_devurl": "https://github.com/darwin-eu/treatmentpatterns",
  "_pkgdown": "https://darwin-eu-dev.github.io/TreatmentPatterns/",
  "_searchresults": 128,
  "_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/readme.html",
    "extra/readme.md",
    "extra/TreatmentPatterns.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/darwin-eu/treatmentpatterns",
  "_realowner": "darwin-eu",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2.5.0",
      "date": "2023-08-16"
    },
    {
      "version": "2.5.1",
      "date": "2023-09-07"
    },
    {
      "version": "2.5.2",
      "date": "2023-09-15"
    },
    {
      "version": "2.6.0",
      "date": "2023-11-13"
    },
    {
      "version": "2.6.1",
      "date": "2023-12-11"
    },
    {
      "version": "2.6.2",
      "date": "2023-12-13"
    },
    {
      "version": "2.6.3",
      "date": "2024-01-25"
    },
    {
      "version": "2.6.4",
      "date": "2024-01-26"
    },
    {
      "version": "2.6.5",
      "date": "2024-02-19"
    },
    {
      "version": "2.6.6",
      "date": "2024-04-16"
    },
    {
      "version": "2.6.7",
      "date": "2024-05-24"
    },
    {
      "version": "2.6.8",
      "date": "2024-08-29"
    },
    {
      "version": "2.6.9",
      "date": "2024-09-02"
    },
    {
      "version": "2.7.0",
      "date": "2024-11-27"
    },
    {
      "version": "3.0.0",
      "date": "2025-02-06"
    },
    {
      "version": "3.0.1",
      "date": "2025-03-10"
    },
    {
      "version": "3.0.2",
      "date": "2025-04-04"
    },
    {
      "version": "3.0.3",
      "date": "2025-04-16"
    },
    {
      "version": "3.1.0",
      "date": "2025-06-03"
    },
    {
      "version": "3.1.1",
      "date": "2025-08-25"
    },
    {
      "version": "3.1.2",
      "date": "2026-02-16"
    }
  ],
  "_exports": [
    "computePathways",
    "createSankeyDiagram",
    "createSunburstPlot",
    "executeTreatmentPatterns",
    "export",
    "exportPatientLevel",
    "getResultsDataModelSpecifications",
    "ggSunburst",
    "plotEventDuration",
    "TreatmentPatternsResults"
  ],
  "_help": [
    {
      "page": "computePathways",
      "title": "computePathways",
      "topics": [
        "computePathways"
      ]
    },
    {
      "page": "createSankeyDiagram",
      "title": "createSankeyDiagram",
      "topics": [
        "createSankeyDiagram"
      ]
    },
    {
      "page": "createSunburstPlot",
      "title": "createSunburstPlot",
      "topics": [
        "createSunburstPlot"
      ]
    },
    {
      "page": "doEraCollapseNew",
      "title": "doEraCollapseNew",
      "topics": [
        "doEraCollapseNew"
      ]
    },
    {
      "page": "executeTreatmentPatterns",
      "title": "executeTreatmentPatterns",
      "topics": [
        "executeTreatmentPatterns"
      ]
    },
    {
      "page": "export",
      "title": "export",
      "topics": [
        "export"
      ]
    },
    {
      "page": "exportPatientLevel",
      "title": "exportPatientLevel",
      "topics": [
        "exportPatientLevel"
      ]
    },
    {
      "page": "getResultsDataModelSpecifications",
      "title": "getResultsDataModelSpecifications",
      "topics": [
        "getResultsDataModelSpecifications"
      ]
    },
    {
      "page": "ggSunburst",
      "title": "ggSunburst",
      "topics": [
        "ggSunburst"
      ]
    },
    {
      "page": "plotEventDuration",
      "title": "plotEventDuration",
      "topics": [
        "plotEventDuration"
      ]
    },
    {
      "page": "TreatmentPatternsResults",
      "title": "TreatmentPatternsResults Class",
      "topics": [
        "TreatmentPatternsResults"
      ]
    }
  ],
  "_readme": "https://github.com/darwin-eu/treatmentpatterns/raw/HEAD/README.md",
  "_rundeps": [
    "Andromeda",
    "askpass",
    "backports",
    "bit",
    "bit64",
    "blob",
    "CDMConnector",
    "checkmate",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "dplyr",
    "duckdb",
    "generics",
    "glue",
    "hms",
    "httr2",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "memuse",
    "omopgenerics",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "readr",
    "rlang",
    "snakecase",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "a000_bestPractices.Rmd",
      "filename": "a000_bestPractices.html",
      "title": "Best practices",
      "author": "Maarten van Kessel",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "TLDR",
        "Cohorts",
        "Combinations",
        "Settings"
      ],
      "created": "2025-06-04 07:39:14",
      "modified": "2025-06-04 07:39:14",
      "commits": 1
    },
    {
      "source": "a010_Computing_Pathways.Rmd",
      "filename": "a010_Computing_Pathways.html",
      "title": "Computing Pathways",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Target and Event cohorts",
        "Database interface",
        "CDMConnector",
        "DatabaseConnector",
        "Analysis",
        "Events",
        "Combinations",
        "Non-Significant Overlap",
        "Overlap Method",
        "Acute and Therapy Splits",
        "Event Windows",
        "Anchoring",
        "windowStart and windowEnd",
        "Changing the anchoring",
        "Pathways",
        "Running the analysis"
      ],
      "created": "2025-06-04 07:39:14",
      "modified": "2025-06-04 07:39:14",
      "commits": 1
    },
    {
      "source": "a998_Strategus.Rmd",
      "filename": "a998_Strategus.html",
      "title": "Strategus Execution",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Database settings",
        "CohortGenerator Module",
        "TreatmentPatterns module",
        "Execution"
      ],
      "created": "2026-02-11 08:22:48",
      "modified": "2026-02-11 08:22:48",
      "commits": 1
    },
    {
      "source": "a001_DefiningCohorts.Rmd",
      "filename": "a001_DefiningCohorts.html",
      "title": "Defining Cohorts",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ATLAS",
        "Cohort information",
        "Viral Sinusitis Cohort parameters",
        "Cohort Entry Events",
        "Inclusion Criteria",
        "Cohort Exit",
        "Cohort Eras",
        "CapR",
        "Cohorts for TreatmentPatterns"
      ],
      "created": "2025-06-04 07:39:14",
      "modified": "2025-06-04 07:39:14",
      "commits": 1
    },
    {
      "source": "a030_Evaluating_Output.Rmd",
      "filename": "a030_Evaluating_Output.html",
      "title": "Evaluating Output",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Saving results",
        "Evaluating Results",
        "treatmentPathways",
        "countsAge, countsSex, and countsYear",
        "summaryStatsTherapyDuration",
        "metadata",
        "Sunburst Plot & Sankey Diagram"
      ],
      "created": "2025-06-04 07:39:14",
      "modified": "2025-08-25 09:30:02",
      "commits": 2
    },
    {
      "source": "a020_Exporting.Rmd",
      "filename": "a020_Exporting.html",
      "title": "Exporing Results",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Exporting result objects",
        "minCellCount and censorType",
        "ageWindow",
        "archiveName",
        "Patient-Level Export"
      ],
      "created": "2025-06-04 07:39:14",
      "modified": "2025-06-04 07:39:14",
      "commits": 1
    },
    {
      "source": "a999_Publications-Presentations.Rmd",
      "filename": "a999_Publications-Presentations.html",
      "title": "Publications and Presentations",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Publications",
        "Presentations"
      ],
      "created": "2026-02-11 08:22:48",
      "modified": "2026-02-11 08:22:48",
      "commits": 1
    }
  ],
  "_score": 7.156427992318051,
  "_indexed": true,
  "_nocasepkg": "treatmentpatterns",
  "_universes": [
    "darwin-eu",
    "mvankessel-emc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1.2",
      "date": "2026-06-19T14:44:40.000Z",
      "distro": "noble",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "fdcf4b82ebd1fe767daa46741548ee73b3578b1e59853b6422d1148478285502",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.1.2",
      "date": "2026-06-19T14:43:47.000Z",
      "distro": "noble",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "b0c58f64b65da72bd2297d955afccce4ad4b1d8d4e062181b56f56f15fefae97",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1.2",
      "date": "2026-06-19T14:42:48.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "39b2a99bd2de4cdc9438a9d137174e54409f37ce5361d8f66e33df86c7b6f83d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.1.2",
      "date": "2026-06-19T14:42:54.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "7834b96cd4d80950ae9896b1b57fb2d3c69bec3f83c531da5944977cadf34064",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.1.2",
      "date": "2026-06-19T14:44:08.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "bdcecf6af4d7bfa5d27171bea181670090fdc57e59843d0a4444fb980c75488e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.1.2",
      "date": "2026-06-19T15:30:18.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "8d32c03a1ce6aca82b1d1a5ab04aae6827c4d9807b69b8ce25233514d268d7de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.1.2",
      "date": "2026-06-19T15:26:19.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "85681efae155809b48dc7495fb4e2cccc7f790a54adb8b8eca221f3206b573a1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.1.2",
      "date": "2026-06-19T15:28:31.000Z",
      "commit": "fb4437f21a1f4c4e495dfc5d42cba869bce1b809",
      "fileid": "e2126c01a1ab86725e8f5798279752a0fca5099de2a9f6d19fd539f011cba0ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/darwin-eu/actions/runs/27831940309"
    }
  ]
}