{ "_id": "6a181496acfb0bcc41daf08a", "Package": "CodelistGenerator", "Title": "Identify Relevant Clinical Codes and Evaluate Their Use", "Version": "4.0.2", "Authors@R": "c(\nperson(\"Edward\", \"Burn\", email = \"edward.burn@ndorms.ox.ac.uk\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9286-1128\")),\nperson( \"Marta\", \"Alcalde-Herraiz\", email = \"marta.alcaldeherraiz@ndorms.ox.ac.uk\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0002-4405-1814\")),\nperson(\"Martí\", \"Català\", email = \"marti.catalasabate@ndorms.ox.ac.uk\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3308-9905\")),\nperson(\"Xihang\", \"Chen\", email = \"xihang.chen@ndorms.ox.ac.uk\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0001-8112-8959\")),\nperson(\"Nuria\", \"Mercade-Besora\", email = \"nuria.mercadebesora@ndorms.ox.ac.uk\",\nrole = c(\"aut\"), comment = c(ORCID = \"0009-0006-7948-3747\")),\nperson(\"Mike\", \"Du\", email = \"mike.du@ndorms.ox.ac.uk\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9517-8834\")),\nperson(\"Danielle\", \"Newby\", email = \"danielle.newby@ndorms.ox.ac.uk\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3001-1478\"))\n)", "Description": "Generate a candidate code list for the Observational\nMedical Outcomes Partnership (OMOP) common data model based on\nstring matching. For a given search strategy, a candidate code\nlist will be returned.", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "VignetteBuilder": "knitr", "URL": "https://darwin-eu.github.io/CodelistGenerator/", "Language": "en-US", "LazyData": "true", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://darwin-eu.r-universe.dev", "Date/Publication": "2026-01-19 19:16:33 UTC", "RemoteUrl": "https://github.com/darwin-eu/codelistgenerator", "RemoteRef": "HEAD", "RemoteSha": "dd643c3a8ea448997d8b800d110b553fe4badbfa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 10:06:21 UTC", "User": "root" }, "Author": "Edward Burn [aut, cre] (ORCID: ),\nMarta Alcalde-Herraiz [aut] (ORCID:\n),\nMartí Català [aut] (ORCID: ),\nXihang Chen [aut] (ORCID: ),\nNuria Mercade-Besora [aut] (ORCID:\n),\nMike Du [aut] (ORCID: ),\nDanielle Newby [aut] (ORCID: )", 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the uses and performance of medicines." }, "_downloads": { "count": 1134, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CodelistGenerator" }, "_devurl": "https://github.com/darwin-eu/codelistgenerator", "_pkgdown": "https://darwin-eu.github.io/CodelistGenerator/", "_searchresults": 378, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CodelistGenerator.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/darwin-eu/codelistgenerator", "_realowner": "darwin-eu", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-02-07" }, { "version": "1.1.0", "date": "2023-04-01" }, { "version": "1.2.0", "date": "2023-05-04" }, { "version": "1.3.0", "date": "2023-05-30" }, { "version": "1.4.0", "date": "2023-06-06" }, { "version": "1.5.0", "date": "2023-06-13" }, { "version": "1.6.0", 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"_exports": [ "addConcepts", "asCodelist", "asCodelistWithDetails", "asConceptSetExpression", "associatedConceptClassIds", "associatedDomains", "associatedDoseForms", "associatedDoseUnits", "associatedDrugIngredients", "associatedRelationshipIds", "associatedRouteCategories", "associatedVocabularies", "availableATC", "availableConceptClassIds", "availableDomains", "availableDoseForms", "availableDoseUnits", "availableDrugIngredients", "availableRelationshipIds", "availableRouteCategories", "availableVocabularies", "benchmarkCodelistGenerator", "codesFromCohort", "codesFromConceptSet", "cohortCodelist", "compareCodelists", "excludeConcepts", "exportCodelist", "exportConceptSetExpression", "getATCCodes", "getCandidateCodes", "getDescendants", "getDrugIngredientCodes", "getMappings", "importCodelist", "importConceptSetExpression", "intersectCodelists", "mockVocabRef", "newCodelist", "newCodelistWithDetails", "newConceptSetExpression", "searchStrategy", "stratifyByBrand", "stratifyByConcept", "stratifyByDomain", "stratifyByDoseForm", "stratifyByDoseUnit", "stratifyByRouteCategory", "stratifyByVocabulary", "subsetOnDomain", "subsetOnDoseForm", "subsetOnDoseUnit", "subsetOnIngredientRange", "subsetOnRouteCategory", "subsetOnVocabulary", "subsetToCodesInUse", "summariseAchillesCodeUse", "summariseCodeUse", "summariseCohortCodeUse", "summariseOrphanCodes", "tableAchillesCodeUse", "tableCodeUse", "tableCohortCodeUse", "tableOrphanCodes", "unionCodelists", "vocabularyVersion" ], "_datasets": [ { "name": "doseFormToRoute", "title": "Table showing the route category associated with each dose form.", "object": "doseFormToRoute", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "dose_form_concept_id", "dose_form_concept_name", "route_category" ], "rows": 194, "table": true, "tojson": true } ], "_help": [ { "page": "addConcepts", "title": "Add concepts to a codelist", "topics": [ "addConcepts" ] }, { "page": "asCodelist", "title": "Coerce to a codelist", "topics": [ "asCodelist", "asCodelist.candidate_codes", "asCodelist.codelist", "asCodelist.codelist_with_details", "asCodelist.concept_set_expression" ] }, { "page": "asCodelistWithDetails", "title": "Coerce to a codelist with details", "topics": [ "asCodelistWithDetails", "asCodelistWithDetails.candidate_codes", "asCodelistWithDetails.codelist", "asCodelistWithDetails.codelist_with_details" ] }, { "page": "asConceptSetExpression", "title": "Coerce to a concept set expression", "topics": [ "asConceptSetExpression", "asConceptSetExpression.codelist", "asConceptSetExpression.codelist_with_details" ] }, { "page": "associatedConceptClassIds", "title": "Get the concept classes associated with a codelist", "topics": [ "associatedConceptClassIds" ] }, { "page": "associatedDomains", "title": "Get the domains associated with a codelist", "topics": [ "associatedDomains" ] }, { "page": "associatedDoseForms", "title": "Get the dose forms associated with drug concepts in a codelist", "topics": [ "associatedDoseForms" ] }, { "page": "associatedDoseUnits", "title": "Get available dose units", "topics": [ "associatedDoseUnits" ] }, { "page": "associatedDrugIngredients", "title": "Get the names of drug ingredients associated with codelist", "topics": [ "associatedDrugIngredients" ] }, { "page": "associatedRelationshipIds", "title": "Get available relationships with concepts in a codelist", "topics": [ "associatedRelationshipIds" ] }, { "page": "associatedRouteCategories", "title": "Get drug routes associated with a codelist", "topics": [ "associatedRouteCategories" ] }, { "page": "associatedVocabularies", "title": "Get the vocabularies associated with a codelist", "topics": [ "associatedVocabularies" ] }, { "page": "availableATC", "title": "Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes", "topics": [ "availableATC" ] }, { "page": "availableConceptClassIds", "title": "Get the available concept classes used in a given set of domains", "topics": [ "availableConceptClassIds" ] }, { "page": "availableDomains", "title": "Get the domains available in the cdm", "topics": [ "availableDomains" ] }, { "page": "availableDoseForms", "title": "Get the dose forms for drug concepts", "topics": [ "availableDoseForms" ] }, { "page": "availableDoseUnits", "title": "Get available dose units", "topics": [ "availableDoseUnits" ] }, { "page": "availableDrugIngredients", "title": "Get the names of all available drug ingredients", "topics": [ "availableDrugIngredients" ] }, { "page": "availableRelationshipIds", "title": "Get available relationships between concepts", "topics": [ "availableRelationshipIds" ] }, { "page": "availableRouteCategories", "title": "Get available drug routes", "topics": [ "availableRouteCategories" ] }, { "page": "availableVocabularies", "title": "Get the available vocabularies available in the cdm", "topics": [ "availableVocabularies" ] }, { "page": "benchmarkCodelistGenerator", "title": "Run benchmark of codelistGenerator analyses", "topics": [ "benchmarkCodelistGenerator" ] }, { "page": "codesFromCohort", "title": "Get concept ids from JSON files containing cohort definitions", "topics": [ "codesFromCohort" ] }, { "page": "codesFromConceptSet", "title": "Get concept ids from JSON files containing concept sets *[Deprecated]*", "topics": [ "codesFromConceptSet" ] }, { "page": "compareCodelists", "title": "Compare overlap between two sets of codes", "topics": [ "compareCodelists" ] }, { "page": "doseFormToRoute", "title": "Table showing the route category associated with each dose form.", "topics": [ "doseFormToRoute" ] }, { "page": "excludeConcepts", "title": "Exclude concepts from a codelist", "topics": [ "excludeConcepts" ] }, { "page": "getATCCodes", "title": "Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes", "topics": [ "getATCCodes" ] }, { "page": "getCandidateCodes", "title": "Perform a systematic search to identify a candidate codelist using the OMOP CDM vocabulary tables.", "topics": [ "getCandidateCodes" ] }, { "page": "getDescendants", "title": "Get descendant codes for a given concept", "topics": [ "getDescendants" ] }, { "page": "getDrugIngredientCodes", "title": "Get descendant codes of drug ingredients", "topics": [ "getDrugIngredientCodes" ] }, { "page": "getMappings", "title": "Show mappings from non-standard vocabularies to standard.", "topics": [ "getMappings" ] }, { "page": "intersectCodelists", "title": "Generate a codelist from the intersection of different codelists. The generated codelist will come out in alphabetical order.", "topics": [ "intersectCodelists" ] }, { "page": "mockVocabRef", "title": "Generate example vocabulary database", "topics": [ "mockVocabRef" ] }, { "page": "searchStrategy", "title": "Report the search strategy used to identify codes when using the 'getCandidateCodes()' function", "topics": [ "searchStrategy" ] }, { "page": "stratifyByBrand", "title": "Stratify a codelist by brand category.", "topics": [ "stratifyByBrand" ] }, { "page": "stratifyByConcept", "title": "Stratify a codelist by the concepts included within it.", "topics": [ "stratifyByConcept" ] }, { "page": "stratifyByDomain", "title": "Stratify a codelist by domain category.", "topics": [ "stratifyByDomain" ] }, { "page": "stratifyByDoseForm", "title": "Stratify a codelist by dose form.", "topics": [ "stratifyByDoseForm" ] }, { "page": "stratifyByDoseUnit", "title": "Stratify a codelist by dose unit.", "topics": [ "stratifyByDoseUnit" ] }, { "page": "stratifyByRouteCategory", "title": "Stratify a codelist by route category.", "topics": [ "stratifyByRouteCategory" ] }, { "page": "stratifyByVocabulary", "title": "Subset a codelist to only those codes from a particular domain.", "topics": [ "stratifyByVocabulary" ] }, { "page": "subsetOnDomain", "title": "Subset a codelist to only those codes from a particular domain.", "topics": [ "subsetOnDomain" ] }, { "page": "subsetOnDoseForm", "title": "Subset a codelist to only those codes from a particular domain.", "topics": [ "subsetOnDoseForm" ] }, { "page": "subsetOnDoseUnit", "title": "Subset a codelist to only those with a particular dose unit.", "topics": [ "subsetOnDoseUnit" ] }, { "page": "subsetOnIngredientRange", "title": "Subset a codelist to only those codes with a range of number of ingredients", "topics": [ "subsetOnIngredientRange" ] }, { "page": "subsetOnRouteCategory", "title": "Subset a codelist to only those with a particular route category", "topics": [ "subsetOnRouteCategory" ] }, { "page": "subsetOnVocabulary", "title": "Subset a codelist to only those codes from a particular vocabulary.", "topics": [ "subsetOnVocabulary" ] }, { "page": "subsetToCodesInUse", "title": "Filter a codelist to keep only the codes being used in patient records", "topics": [ "subsetToCodesInUse" ] }, { "page": "summariseAchillesCodeUse", "title": "Summarise code use from achilles counts.", "topics": [ "summariseAchillesCodeUse" ] }, { "page": "summariseCodeUse", "title": "Summarise code use in patient-level data.", "topics": [ "summariseCodeUse" ] }, { "page": "summariseCohortCodeUse", "title": "Summarise code use among a cohort in the cdm reference", "topics": [ "summariseCohortCodeUse" ] }, { "page": "summariseOrphanCodes", "title": "Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations", "topics": [ "summariseOrphanCodes" ] }, { "page": "tableAchillesCodeUse", "title": "Format the result of summariseAchillesCodeUse into a table", "topics": [ "tableAchillesCodeUse" ] }, { "page": "tableCodeUse", "title": "Format the result of summariseCodeUse into a table.", "topics": [ "tableCodeUse" ] }, { "page": "tableCohortCodeUse", "title": "Format the result of summariseCohortCodeUse into a table.", "topics": [ "tableCohortCodeUse" ] }, { "page": "tableOrphanCodes", "title": "Format the result of summariseOrphanCodes into a table", "topics": [ "tableOrphanCodes" ] }, { "page": "unionCodelists", "title": "Generate a codelist from the union of different codelists. The generated codelist will come out in alphabetical order.", "topics": [ "unionCodelists" ] }, { "page": "vocabularyVersion", "title": "Get the available version of the vocabulary used in the cdm", "topics": [ "vocabularyVersion" ] } ], "_pkglogo": "https://github.com/darwin-eu/codelistgenerator/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/darwin-eu/codelistgenerator/raw/HEAD/README.md", "_rundeps": [ "blob", "cli", "clock", "cpp11", "DBI", "dbplyr", "dplyr", "generics", "glue", "jsonlite", "lifecycle", "magrittr", "omopgenerics", "PatientProfiles", "pillar", "pkgconfig", "purrr", "R6", "rlang", "snakecase", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "a01_GettingOmopCdmVocabularies.Rmd", "filename": "a01_GettingOmopCdmVocabularies.html", "title": "Getting the OMOP CDM vocabularies", "engine": "knitr::rmarkdown", "headings": [ "Connect to an existing OMOP CDM database", "Create a local 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