Package: CodelistGenerator 3.2.1

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], Marti Catala [ctb], Xihang Chen [aut], Nuria Mercade-Besora [aut], Mike Du [ctb], Danielle Newby [ctb]

CodelistGenerator_3.2.1.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'))

Peer review:

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

Datasets:
  • doseFormToRoute - Equivalence from dose from concept IDs to route categories.

On CRAN:

9.55 score 12 stars 3 packages 126 scripts 1.1k downloads 39 exports 49 dependencies

Last updated 20 days agofrom:c849af4b5d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 17 2024
R-4.5-winOKOct 17 2024
R-4.5-linuxOKOct 17 2024
R-4.4-winOKOct 17 2024
R-4.4-macOKOct 17 2024
R-4.3-winOKOct 17 2024
R-4.3-macOKOct 17 2024

Exports:%>%availableATCavailableICD10availableIngredientscodesFromCohortcodesFromConceptSetcodesInUsecompareCodelistsgetATCCodesgetCandidateCodesgetConceptClassIdgetDescendantsgetDomainsgetDoseFormgetDoseUnitgetDrugIngredientCodesgetICD10StandardCodesgetMappingsgetRelationshipIdgetRouteCategoriesgetVocabulariesgetVocabVersionmockVocabRefrestrictToCodesInUsesourceCodesInUsestratifyByConceptstratifyByDoseUnitstratifyByRouteCategorysubsetOnDoseUnitsubsetOnRouteCategorysubsetToCodesInUsesummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodestableAchillesCodeUsetableCodeUsetableCohortCodeUsetableOrphanCodes

Dependencies:backportsbitbit64blobCDMConnectorcheckmateclicliprcpp11crayonDBIdbplyrdiffobjdplyrfansifsgenericsgluehmsjsonlitelifecyclelubridatemagrittromopgenericsPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrematch2RJSONIOrlangsnakecasestringistringrtibbletidyrtidyselecttimechangetzdbutf8vctrsvisOmopResultsvroomwaldowithr

Introduction to CodelistGenerator

Rendered froma01_Introduction_to_CodelistGenerator.Rmdusingknitr::rmarkdownon Oct 17 2024.

Last update: 2024-01-24
Started: 2022-05-14

CodelistGenerator options: examples with a with mock vocabulary

Rendered froma03_Options_for_CodelistGenerator.Rmdusingknitr::rmarkdownon Oct 17 2024.

Last update: 2024-02-07
Started: 2022-09-18

CodelistGenerator search options: codes for osteoarthritis

Rendered froma02_Candidate_codes_OA.Rmdusingknitr::rmarkdownon Oct 17 2024.

Last update: 2024-01-24
Started: 2023-02-07

Generating vocabulary based codelists

Rendered froma04_Vocab_based_codelists.Rmdusingknitr::rmarkdownon Oct 17 2024.

Last update: 2024-07-10
Started: 2024-04-12

Readme and manuals

Help Manual

Help pageTopics
Get all ATC codes from the cdmavailableATC
Get all ICD codes from the cdmavailableICD10
Get all ingredients codes from the cdmavailableIngredients
Get concept ids from a provided path to cohort json filescodesFromCohort
Get concept ids from a provided path to json filescodesFromConceptSet
Use achilles counts to get codes used in the databasecodesInUse
Compare two codelistscompareCodelists
Equivalence from dose from concept IDs to route categories.doseFormToRoute
Get descendant codes for ATC levelsgetATCCodes
Generate candidate codelist for the OMOP CDMgetCandidateCodes
getConceptClassIdgetConceptClassId
getDescendantsgetDescendants
getDomainsgetDomains
getDoseFormgetDoseForm
Get available routes in a cdm reference.getDoseUnit
Get descendant codes for drug ingredientsgetDrugIngredientCodes
Get corresponding standard codes for ICD-10 chapters and sub-chaptersgetICD10StandardCodes
Show mappings from non-standard vocabularies to standardgetMappings
Get relationship ID values from the concept relationship tablegetRelationshipId
Get available routes in a cdm reference.getRouteCategories
getVocabulariesgetVocabularies
getVocabVersiongetVocabVersion
Generate example vocabulary databasemockVocabRef
Use achilles counts to filter a codelist to keep only the codes used in the databaserestrictToCodesInUse
Use achilles counts to get source codes used in the databasesourceCodesInUse
Stratify a codelist by the concepts included within itstratifyByConcept
Stratify a codelist by dose unitstratifyByDoseUnit
Stratify a codelist by route categorystratifyByRouteCategory
Subset a codelist to only those with a particular dose unitsubsetOnDoseUnit
Subset a codelist to only those with a particular route categorysubsetOnRouteCategory
Use achilles counts to filter a codelist to keep only the codes used in the databasesubsetToCodesInUse
Summarise code use from achilles countssummariseAchillesCodeUse
Summarise code use in patient-level datasummariseCodeUse
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 table.tableAchillesCodeUse
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 table.tableOrphanCodes