Package: CodelistGenerator 3.3.0

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

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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

Datasets:

doseFormToRoute - Equivalence from dose from concept IDs to route categories.

On CRAN:

9.56 score 12 stars 3 packages 108 scripts 1.2k downloads 41 exports 48 dependencies

Last updated 8 days agofrom:8fb5d0b0db. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-win	OK	Nov 11 2024
R-4.5-linux	OK	Nov 11 2024
R-4.4-win	OK	Nov 11 2024
R-4.4-mac	OK	Nov 11 2024
R-4.3-win	OK	Nov 11 2024
R-4.3-mac	OK	Nov 11 2024

Exports:%>%availableATC availableICD10 availableIngredients codesFromCohort codesFromConceptSet codesInUse compareCodelists getATCCodes getCandidateCodes getConceptClassId getDescendants getDomains getDoseForm getDoseUnit getDrugIngredientCodes getICD10StandardCodes getMappings getRelationshipId getRouteCategories getVocabularies getVocabVersion mockVocabRef sourceCodesInUse stratifyByConcept stratifyByDoseUnit stratifyByRouteCategory subsetOnDomain subsetOnDoseUnit subsetOnRouteCategory subsetToCodesInUse summariseAchillesCodeUse summariseCodeUse summariseCohortCodeUse summariseOrphanCodes summariseUnmappedCodes tableAchillesCodeUse tableCodeUse tableCohortCodeUse tableOrphanCodes tableUnmappedCodes

Dependencies:backports bit bit64 blob CDMConnector checkmate cli clipr cpp11 crayon DBI dbplyr diffobj dplyr fansi fs generics glue hms jsonlite lifecycle lubridate magrittr omopgenerics PatientProfiles pillar pkgconfig prettyunits progress purrr R6 readr RJSONIO rlang snakecase stringi stringr tibble tidyr tidyselect timechange tzdb utf8 vctrs visOmopResults vroom waldo withr

Introduction to CodelistGenerator

Rendered froma01_Introduction_to_CodelistGenerator.Rmdusingknitr::rmarkdownon Nov 11 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 Nov 11 2024.

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

CodelistGenerator search options: codes for osteoarthritis

Rendered froma02_Candidate_codes_OA.Rmdusingknitr::rmarkdownon Nov 11 2024.

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

Generating vocabulary based codelists

Rendered froma04_Vocab_based_codelists.Rmdusingknitr::rmarkdownon Nov 11 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get all ATC codes from the cdm	availableATC
Get all ICD codes from the cdm	availableICD10
Get all ingredients codes from the cdm	availableIngredients
Get concept ids from a provided path to cohort json files	codesFromCohort
Get concept ids from a provided path to json files	codesFromConceptSet
Use achilles counts to get codes used in the database	codesInUse
Compare two codelists	compareCodelists
Equivalence from dose from concept IDs to route categories.	doseFormToRoute
Get descendant codes for ATC levels	getATCCodes
Generate candidate codelist for the OMOP CDM	getCandidateCodes
getConceptClassId	getConceptClassId
getDescendants	getDescendants
getDomains	getDomains
getDoseForm	getDoseForm
Get available routes in a cdm reference.	getDoseUnit
Get descendant codes for drug ingredients	getDrugIngredientCodes
Get corresponding standard codes for ICD-10 chapters and sub-chapters	getICD10StandardCodes
Show mappings from non-standard vocabularies to standard	getMappings
Get relationship ID values from the concept relationship table	getRelationshipId
Get available routes in a cdm reference.	getRouteCategories
getVocabularies	getVocabularies
getVocabVersion	getVocabVersion
Generate example vocabulary database	mockVocabRef
Use achilles counts to get source codes used in the database	sourceCodesInUse
Stratify a codelist by the concepts included within it	stratifyByConcept
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	subsetOnDomain
Subset a codelist to only those with a particular dose unit	subsetOnDoseUnit
Subset a codelist to only those with a particular route category	subsetOnRouteCategory
Use achilles counts to filter a codelist to keep only the codes used in the database	subsetToCodesInUse
Summarise code use from achilles counts	summariseAchillesCodeUse
Summarise code use in patient-level data	summariseCodeUse
Summarise code use among a cohort in the cdm reference	summariseCohortCodeUse
Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations	summariseOrphanCodes
Findunmapped concepts related to codelist	summariseUnmappedCodes
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
Format the result of summariseUnmappedCodeUse into a table.	tableUnmappedCodes