Package: CodelistGenerator 4.0.0

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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_4.0.0.tar.gz
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CodelistGenerator.pdf |CodelistGenerator.html✨
CodelistGenerator/json (API)
NEWS

# 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:

9.97 score 17 stars 4 packages 293 scripts 770 downloads 66 exports 29 dependencies

Last updated from:388c11e0a5. Checks:8 OK. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-x86_64OK196
source / vignettesOK457
macos-devel-arm64OK343
macos-release-arm64OK410
windows-develOK154
windows-releaseOK138
windows-oldrelOK197
wasm-releaseOK204

Exports:addConceptsasCodelistasCodelistWithDetailsasConceptSetExpressionassociatedConceptClassIdsassociatedDomainsassociatedDoseFormsassociatedDoseUnitsassociatedDrugIngredientsassociatedRelationshipIdsassociatedRouteCategoriesassociatedVocabulariesavailableATCavailableConceptClassIdsavailableDomainsavailableDoseFormsavailableDoseUnitsavailableDrugIngredientsavailableRelationshipIdsavailableRouteCategoriesavailableVocabulariesbenchmarkCodelistGeneratorcodesFromCohortcodesFromConceptSetcohortCodelistcompareCodelistsexcludeConceptsexportCodelistexportConceptSetExpressiongetATCCodesgetCandidateCodesgetDescendantsgetDrugIngredientCodesgetMappingsimportCodelistimportConceptSetExpressionintersectCodelistsmockVocabRefnewCodelistnewCodelistWithDetailsnewConceptSetExpressionsearchStrategystratifyByBrandstratifyByConceptstratifyByDomainstratifyByDoseFormstratifyByDoseUnitstratifyByRouteCategorystratifyByVocabularysubsetOnDomainsubsetOnDoseFormsubsetOnDoseUnitsubsetOnIngredientRangesubsetOnRouteCategorysubsetOnVocabularysubsetToCodesInUsesummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodestableAchillesCodeUsetableCodeUsetableCohortCodeUsetableOrphanCodesunionCodelistsvocabularyVersion

Dependencies:blobcliclockcpp11DBIdbplyrdplyrgenericsgluejsonlitelifecyclemagrittromopgenericsPatientProfilespillarpkgconfigpurrrR6rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrswithr

Getting the OMOP CDM vocabularies

Rendered froma01_GettingOmopCdmVocabularies.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Exploring the OMOP CDM vocabulary tables

Rendered froma02_ExploreCDMvocabulary.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Types of Codelist

Rendered froma03_TypesOfCodelist.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Generate a candidate codelist

Rendered froma04_GenerateCandidateCodelist.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Generating vocabulary based codelists for medications

Rendered froma05_GenerateVocabularyBasedCodelist.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Importing and exporting codelists

Rendered froma06_ImportExport.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Manipulate codelists

Rendered froma08_ManipulateCodelists.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Codelist diagnostics

Rendered froma09_RunCodelistDiagnostics.Rmdusingknitr::rmarkdownon Dec 18 2025.

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

Benchmarking the CodelistGenerator R package

Rendered froma10_CodelistGeneratorBenchmark.Rmdusingknitr::rmarkdownon Dec 18 2025.

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 available relationships with concepts in a codelistassociatedRelationshipIds
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
Exclude concepts from a codelistexcludeConcepts
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
Generate a codelist from the intersection of different codelists. The generated codelist will come out in alphabetical order.intersectCodelists
Generate example vocabulary databasemockVocabRef
Report the search strategy used to identify codes when using the 'getCandidateCodes()' functionsearchStrategy
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
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