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.

Version: 3.5.0
Depends: R (≥ 4.1)
Imports: DBI (≥ 1.1.0), dplyr (≥ 1.1.0), omopgenerics (≥ 1.1.1), rlang (≥ 1.0.0), glue (≥ 1.5.0), stringr (≥ 1.4.0), stringi (≥ 1.8.1), tidyr (≥ 1.2.0), cli (≥ 3.1.0), purrr, clock, PatientProfiles (≥ 1.3.1), vctrs, jsonlite, lifecycle
Suggests: covr, duckdb, CDMConnector (≥ 1.7.0), visOmopResults (≥ 1.0.0), knitr, rmarkdown, testthat (≥ 3.0.0), RPostgres, odbc, spelling, tibble, gt, flextable, omock, CohortConstructor
Published: 2025-04-10
DOI: 10.32614/CRAN.package.CodelistGenerator
Author: Edward Burn ORCID iD [aut, cre], Marti Catala ORCID iD [ctb], Xihang Chen ORCID iD [aut], Nuria Mercade-Besora ORCID iD [aut], Mike Du ORCID iD [ctb], Danielle Newby ORCID iD [ctb], Marta Alcalde-Herraiz ORCID iD [ctb]
Maintainer: Edward Burn <edward.burn at ndorms.ox.ac.uk>
License: Apache License (≥ 2)
URL: https://darwin-eu.github.io/CodelistGenerator/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
CRAN checks: CodelistGenerator results

Documentation:

Reference manual: CodelistGenerator.pdf
Vignettes: a01_GettingOmopCdmVocabularies (source, R code)
a02_ExploreCDMvocabulary (source, R code)
a03_GenerateCandidateCodelist (source, R code)
a04_GenerateVocabularyBasedCodelist (source, R code)
a04b_icd_codes (source, R code)
a05_ExtractCodelistsfromJSONfile (source, R code)
a06_CreateSubsetsFromCodelist (source, R code)
a07_RunCodelistDiagnostics (source, R code)

Downloads:

Package source: CodelistGenerator_3.5.0.tar.gz
Windows binaries: r-devel: CodelistGenerator_3.4.1.zip, r-release: CodelistGenerator_3.4.1.zip, r-oldrel: CodelistGenerator_3.4.1.zip
macOS binaries: r-devel (arm64): CodelistGenerator_3.5.0.tgz, r-release (arm64): CodelistGenerator_3.5.0.tgz, r-oldrel (arm64): CodelistGenerator_3.5.0.tgz, r-devel (x86_64): CodelistGenerator_3.5.0.tgz, r-release (x86_64): CodelistGenerator_3.5.0.tgz, r-oldrel (x86_64): CodelistGenerator_3.5.0.tgz
Old sources: CodelistGenerator archive

Reverse dependencies:

Reverse imports: CohortSymmetry, DrugUtilisation, PhenotypeR
Reverse suggests: CohortCharacteristics, CohortConstructor, CohortSurvival, OmopSketch, OmopViewer, PatientProfiles

Linking:

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