Files in oxford-pharmacoepi/CodelistGenerator

Identify Relevant Clinical Codes and Evaluate Their Use

.Rbuildignore

.github/.gitignore

.github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/lint.yaml

.github/workflows/pkgdown.yaml

.github/workflows/r-cmd-check-ubuntu.yaml

.gitignore

CodelistGenerator.Rproj

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/CodelistGenerator-package.R R/achillesCodeUse.R R/checks.R R/codesFromConceptSet.R R/codesInUse.R R/compareCodelists.R R/drugCodes.R R/findOrphanCodes.R R/findUnmappedCodes.R R/getCandidateCodes.R R/getICD10StandardCodes.R R/getMappings.R R/inputValidation.R R/mockVocabRef.R R/runSearch.R R/summariseCodeUse.R R/utils-pipe.R R/vocabUtilities.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran-comments.md

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/README.knit.html

docs/articles/Introduction_to_CodelistGenerator.html

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/css/crosstalk.min.css

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/js/crosstalk.js

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/js/crosstalk.js.map

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/js/crosstalk.min.js

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/js/crosstalk.min.js.map

docs/articles/Introduction_to_CodelistGenerator_files/crosstalk-1.2.0/scss/crosstalk.scss

docs/articles/Introduction_to_CodelistGenerator_files/datatables-binding-0.21/datatables.js

docs/articles/Introduction_to_CodelistGenerator_files/datatables-css-0.0.0/datatables-crosstalk.css

docs/articles/Introduction_to_CodelistGenerator_files/dt-core-1.11.3/css/jquery.dataTables.extra.css

docs/articles/Introduction_to_CodelistGenerator_files/dt-core-1.11.3/css/jquery.dataTables.min.css

docs/articles/Introduction_to_CodelistGenerator_files/dt-core-1.11.3/js/jquery.dataTables.min.js

docs/articles/Introduction_to_CodelistGenerator_files/htmlwidgets-1.5.4/htmlwidgets.js

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/clean_words.html

docs/reference/figures/README-pressure-1.png

docs/reference/get_candidate_codes.html

docs/reference/index.html

docs/reference/show_mappings.html

docs/sitemap.xml

extras/MockDbCodelistGenerator.drawio

extras/precomputeVignetteData.R

inst/WORDLIST

inst/cohorts/cohorts.json

inst/cohorts/extra_file.txt

inst/cohorts_for_mock/oa_desc.json

inst/cohorts_for_mock/oa_no_desc.json

inst/cohorts_for_mock_dups/oa_desc.json

inst/cohorts_for_mock_dups/oa_no_desc.json

inst/cohorts_for_mock_with_exclude/oa_desc.json

inst/cohorts_for_mock_with_mapped/oa_desc.json

inst/cohorts_for_mock_with_mapped/oa_no_desc.json

inst/concepts/acetaminophen.json

inst/concepts/extra_file.txt

inst/concepts/influenza.json

inst/concepts_for_mock/oa_desc.json

inst/concepts_for_mock/oa_no_desc.json

inst/concepts_for_mock_with_exclude/oa_desc.json

inst/concepts_for_mock_with_exclude/oa_with_excluded.json

inst/concepts_for_mock_with_exclude/oa_with_excluded2.json

inst/concepts_for_mock_with_mapped/oa_desc.json

inst/concepts_for_mock_with_mapped/oa_with_mapped.json

inst/introData01.RData

inst/introData02.RData

inst/introData03.RData

inst/introData04.RData

inst/introData05.RData

inst/introVocab.RData

inst/medData01.RData

inst/medData02a.RData

inst/medData02b.RData

inst/medData03.RData

inst/medDataConceptClass.RData

inst/medDataDoseForms.RData

inst/not_all_concept_sets/acetaminophen.json

inst/not_all_concept_sets/cohort_def.json

inst/not_all_concept_sets/influenza.json

inst/optionsData01.RData

inst/optionsData02.RData

inst/optionsData03.RData

inst/optionsData04.RData

inst/optionsData05.RData

inst/optionsData06.RData

inst/optionsData07.RData

man/CodelistGenerator-package.Rd man/achillesCodeUse.Rd man/codesFromCohort.Rd man/codesFromConceptSet.Rd man/codesInUse.Rd man/compareCodelists.Rd

man/figures/hexsticker.png

man/findOrphanCodes.Rd man/getATCCodes.Rd man/getCandidateCodes.Rd man/getConceptClassId.Rd man/getDescendants.Rd man/getDomains.Rd man/getDoseForm.Rd man/getDrugIngredientCodes.Rd man/getICD10StandardCodes.Rd man/getMappings.Rd man/getRelationshipId.Rd man/getVocabVersion.Rd man/getVocabularies.Rd man/mockVocabRef.Rd man/pipe.Rd man/restrictToCodesInUse.Rd man/sourceCodesInUse.Rd man/summariseCodeUse.Rd man/summariseCohortCodeUse.Rd tests/testthat.R tests/testthat/test-achillesCodeUse.R tests/testthat/test-codesFrom.R tests/testthat/test-codesInUse.R tests/testthat/test-compareCodelists.R tests/testthat/test-dbms.R tests/testthat/test-drugCodes.R tests/testthat/test-findOrphanCodes.R tests/testthat/test-findUnmappedCodes.R tests/testthat/test-getCandidateCodes.R tests/testthat/test-getICD10StandardCodes.R tests/testthat/test-getMappings.R tests/testthat/test-mockVocabRef.R tests/testthat/test-summariseCodeUse.R tests/testthat/test-synthea_sql_server.R tests/testthat/test-tidyWords.R tests/testthat/test-vocabUtilities.R

vignettes/.gitignore

vignettes/a01_Introduction_to_CodelistGenerator.Rmd vignettes/a02_Candidate_codes_OA.Rmd vignettes/a03_Options_for_CodelistGenerator.Rmd vignettes/a04_Vocab_based_codelists.Rmd

vignettes/mock_db_fig1.png

vignettes/mock_db_fig2.png

vignettes/mock_db_fig3.png

vignettes/mock_db_fig4.png

vignettes/mock_db_fig5.png

vignettes/mock_db_fig6.png

vignettes/mock_db_fig7.png

vignettes/mock_db_fig8.png

oxford-pharmacoepi/CodelistGenerator documentation built on April 12, 2024, 9:30 a.m.