Package: CodelistGenerator 4.1.0

Edward Burn

CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.

Authors:Edward Burn [aut, cre], Marta Alcalde-Herraiz [aut], Martí Català [aut], Xihang Chen [aut], Nuria Mercade-Besora [aut], Mike Du [aut], Danielle Newby [aut]

CodelistGenerator_4.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CodelistGenerator/json (API)

# Install 'CodelistGenerator' in R:
install.packages('CodelistGenerator', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/codelistgenerator/issues

Pkgdown/docs site:https://darwin-eu.github.io

Datasets:
  • doseFormToRoute - Table showing the route category associated with each dose form.

On CRAN:

Conda:

10.50 score 18 stars 7 packages 366 scripts 1.8k downloads 69 exports 28 dependencies

Last updated from:7628b4e6fc. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK208
source / vignettesOK259
linux-releaseOK192
macos-releaseOK154
macos-oldrelOK155
windows-develOK154
windows-releaseOK128
windows-oldrelOK138
wasm-releaseOK140

Exports:addConceptsasCodelistasCodelistWithDetailsasConceptSetExpressionassociatedConceptClassIdsassociatedDomainsassociatedDoseFormsassociatedDoseUnitsassociatedDrugIngredientsassociatedRelationshipIdsassociatedRouteCategoriesassociatedVocabulariesavailableATCavailableConceptClassIdsavailableDomainsavailableDoseFormsavailableDoseUnitsavailableDrugIngredientsavailableRelationshipIdsavailableRouteCategoriesavailableVocabulariesbenchmarkCodelistGeneratorcodesFromCohortcodesFromConceptSetcohortCodelistcompareCodelistsemptyCodeSearchexcludeConceptsexportCodelistexportCodeSearchexportConceptSetExpressiongetATCCodesgetCandidateCodesgetDescendantsgetDrugIngredientCodesgetMappingsimportCodelistimportCodeSearchimportConceptSetExpressionintersectCodelistsmockVocabRefnewCodelistnewCodelistWithDetailsnewConceptSetExpressionsearchStrategystratifyByBrandstratifyByConceptstratifyByDomainstratifyByDoseFormstratifyByDoseUnitstratifyByRouteCategorystratifyByVocabularysubsetOnDomainsubsetOnDoseFormsubsetOnDoseUnitsubsetOnIngredientRangesubsetOnRouteCategorysubsetOnVocabularysubsetToCodesInUsesummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodestableAchillesCodeUsetableCodeUsetableCohortCodeUsetableOrphanCodesunionCodelistsvocabularyVersion

Dependencies:blobcliclockcpp11DBIdbplyrdplyrgenericsgluelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigpurrrR6rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrswithr

Getting the OMOP CDM vocabularies
Connect to an existing OMOP CDM database | Create a local vocabulary database | Download vocabularies from athena | Create a duckdb database
Rendered froma01_GettingOmopCdmVocabularies.Rmdusingknitr::rmarkdown

Last update: 2026-08-01
Started: 2025-04-11

Types of Codelist
Codelist | Create an empty codelist | Codelist with details | Create an empty codelist with details | Concept set expression | Create an empty concept set expression | Concept set expression from a JSON file | Change to different codelist types | Codelist/Concept set expression to codelist with details | Codelist/Codelist with details to concept set expression | Codelist with details/Concept set expression to codelist
Rendered froma03_TypesOfCodelist.Rmdusingknitr::rmarkdown

Last update: 2026-08-01
Started: 2025-12-18

Generate a candidate codelist
Search for keyword match | Include non-standard concepts | Multiple search terms | Add descendants | With exclusions | Search using synonyms | Search via non-standard
Rendered froma04_GenerateCandidateCodelist.Rmdusingknitr::rmarkdown

Last update: 2026-08-01
Started: 2025-12-18

Exploring the OMOP CDM vocabulary tables
Vocabulary characteristics | Domains | Concept class | Relationships
Rendered froma02_ExploreCDMvocabulary.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-04-11

Generating vocabulary based codelists for medications
Ingredient based codelists | Restrict to a specific dose form | Restrict to a specific dose unit | Restrict to a specific route | Search multiple ingredients | ATC based codelists
Rendered froma05_GenerateVocabularyBasedCodelist.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-12-18

Importing and exporting codelists
Importing concept sets
Rendered froma06_ImportExport.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-12-18

Manipulate codelists
Introduction: Manipulate codelists | Subsetting a Codelist | Subset by Domain | Subset on vocabulary | Subset on Dose Unit | Subset on ingredient range | Subset on route category | Subset on dose forms | Stratify codelist | Stratify by Dose Unit | Stratify by Route Category | Stratify by Dose Form | Add or remove concepts from a codelist | Codelist construction | Compare codelists
Rendered froma08_ManipulateCodelists.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-12-18

Codelist diagnostics
Running diagnostics for a codelist | Summarise code use using ACHILLES tables | Summarise code use using patient-level data | Identify orphan codes | Run diagnostics within a cohort | Summarise code use at cohort entry | Cohort code use with a different codelist | Stratify cohort code use
Rendered froma09_RunCodelistDiagnostics.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-12-18

Benchmarking the CodelistGenerator R package
Rendered froma10_CodelistGeneratorBenchmark.Rmdusingknitr::rmarkdown

Last update: 2025-12-18
Started: 2025-12-18

Readme and manuals

Help Manual

Help pageTopics
Add concepts to a codelistaddConcepts
Coerce to a codelistasCodelist asCodelist.candidate_codes asCodelist.codelist asCodelist.codelist_with_details asCodelist.concept_set_expression
Coerce to a codelist with detailsasCodelistWithDetails asCodelistWithDetails.candidate_codes asCodelistWithDetails.codelist asCodelistWithDetails.codelist_with_details
Coerce to a concept set expressionasConceptSetExpression asConceptSetExpression.codelist asConceptSetExpression.codelist_with_details
Get the concept classes associated with a codelistassociatedConceptClassIds
Get the domains associated with a codelistassociatedDomains
Get the dose forms associated with drug concepts in a codelistassociatedDoseForms
Get available dose unitsassociatedDoseUnits
Get the names of drug ingredients associated with codelistassociatedDrugIngredients
Get all relationships types that exist in the OMOP vocabulary 'concept_relationship' table for a given set of concepts in a codelist.associatedRelationshipIds
Get drug routes associated with a codelistassociatedRouteCategories
Get the vocabularies associated with a codelistassociatedVocabularies
Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codesavailableATC
Get the available concept classes used in a given set of domainsavailableConceptClassIds
Get the domains available in the cdmavailableDomains
Get the dose forms for drug conceptsavailableDoseForms
Get available dose unitsavailableDoseUnits
Get the names of all available drug ingredientsavailableDrugIngredients
Get available relationships between conceptsavailableRelationshipIds
Get available drug routesavailableRouteCategories
Get the available vocabularies available in the cdmavailableVocabularies
Run benchmark of codelistGenerator analysesbenchmarkCodelistGenerator
Get concept ids from JSON files containing cohort definitionscodesFromCohort
Get concept ids from JSON files containing concept sets *[Deprecated]*codesFromConceptSet
Compare overlap between two sets of codescompareCodelists
Table showing the route category associated with each dose form.doseFormToRoute
Empty code search objectemptyCodeSearch
Exclude concepts from a codelistexcludeConcepts
Export a 'code_search' object into an Excel spreadsheetexportCodeSearch
Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codesgetATCCodes
Perform a systematic search to identify a candidate codelist using the OMOP CDM vocabulary tables.getCandidateCodes
Get descendant codes for a given conceptgetDescendants
Get descendant codes of drug ingredientsgetDrugIngredientCodes
Show mappings from non-standard vocabularies to standard.getMappings
Import a 'code_search' object from an Excel spreadsheetimportCodeSearch
Generate a codelist from the intersection of different codelists. The generated codelist will come out in alphabetical order.intersectCodelists
Generate example vocabulary databasemockVocabRef
Create a new 'code_search' objectnewCodeSearch
Get the search strategy used to create a certain code_searchsearchStrategy
Stratify a codelist by brand category.stratifyByBrand
Stratify a codelist by the concepts included within it.stratifyByConcept
Stratify a codelist by domain category.stratifyByDomain
Stratify a codelist by dose form.stratifyByDoseForm
Stratify a codelist by dose unit.stratifyByDoseUnit
Stratify a codelist by route category.stratifyByRouteCategory
Subset a codelist to only those codes from a particular domain.stratifyByVocabulary
Subset a codelist to only those codes from a particular domain.subsetOnDomain
Subset a codelist to only those codes from a particular domain.subsetOnDoseForm
Subset a codelist to only those with a particular dose unit.subsetOnDoseUnit
Subset a codelist to only those codes with a range of number of ingredientssubsetOnIngredientRange
Subset a codelist to only those with a particular route categorysubsetOnRouteCategory
Subset a codelist to only those codes from a particular vocabulary.subsetOnVocabulary
Filter a codelist to keep only the codes being used in patient recordssubsetToCodesInUse
Summarise code use from achilles counts.summariseAchillesCodeUse
Summarise code use in patient-level data.summariseCodeUse
Summarise code use among a cohort in the cdm referencesummariseCohortCodeUse
Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendationssummariseOrphanCodes
Format the result of summariseAchillesCodeUse into a tabletableAchillesCodeUse
Format the result of summariseCodeUse into a table.tableCodeUse
Format the result of summariseCohortCodeUse into a table.tableCohortCodeUse
Format the result of summariseOrphanCodes into a tabletableOrphanCodes
Generate a codelist from the union of different codelists. The generated codelist will come out in alphabetical order.unionCodelists
Get the available version of the vocabulary used in the cdmvocabularyVersion