Package index • ROMOPMappingTools

All functions

LogTibble: LogTibble

STCMToCDMTables(): Convert Source to Concept Map to CDM Tables

appendUsagiFileToSTCMtable(): Append Usagi File to Source to Concept Map Table

autoFixDatabaseCodeCountsFile(): autoFixDatabaseCodeCountTable

buildStatusDashboard(): Build Status Dashboard

buildUpdateStatusMd(): Build Update Status Markdown

buildValidationStatusMd(): Build Validation Status Markdown

buildVocabulariesAll(): Run All Validation and Upload Steps

calculateMappingStatus(): calculateMappingStatus

conceptRelationshipToAncestorTables(): Convert CONCEPT_RELATIONSHIP to CONCEPT_ANCESTOR

createSourceToConceptMapExtended(): Create Extended Source to Concept Map Table

.background_bar_reactable_style(): Render a bar chart in the background of the cell

.getCodeCountsForVocabularyAndDatabase(): Get code counts for a vocabulary and database

.getDatabaseSummaryForVocabulary(): Get database summary for a vocabulary

.getSummaryListForVocabulary(): Get summary list for a vocabulary

.getSummaryTableForVocabularyAndDatabase(): Get summary table for a vocabulary and database

.getUsagiSummaryForVocabulary(): Get Usagi summary for a vocabulary

.pageCoverageVocabularyDatabases(): Render coverage page for a vocabulary and its databases

.pageSummaryAllVocabularies(): Render summary page for all vocabularies

.plotSummaryTableForUsagiFile(): Plot summary table for Usagi file

.plotSummaryTableForVocabularyAndDatabase(): Plot summary table for a vocabulary and database

.plotTableForUsagiFile(): Plot Usagi file table

.plotTableForVocabularyAndDatabase(): Plot detailed table for a vocabulary and database

.plotTableSummaryAllVocabularies(): Plot summary table for all vocabularies

.tip_reactable_cell(): Tooltip for reactable cell

duckdbToOMOPVocabularyCSVs(): Export vocabulary tables from a database to CSV files

helper_createATemporaryCopyOfTheOMOPVocabularyDuckDB(): Create a Temporary Copy of the OMOP Vocabulary DuckDB

omopVocabularyCSVsToDuckDB(): Convert OMOP Vocabulary CSVs to Database

plotTableMappingStatus(): tableMappingStatus

plotTableVocabularyStatus(): Plot Table Vocabulary Status

readUsagiFile(): Read Usagi File

updateUsagiFile(): Validate Usagi File

updateVocabularyFolder(): Update Vocabulary Folder

validateCDMtablesWithDQD(): Validate CDM Tables Using Data Quality Dashboard

validateCodeCountsFile(): Validate Code Counts Folder

validateCodeCountsFolder(): Validate Code Counts Folder

validateUsagiFile(): Validate Usagi File

validateVocabularyFolder(): Validate Vocabulary Folder

vocabularyFolderToSTCMVocabularyConcepClassTables(): Upload Vocabulary Folder to CDM Tables

writeUsagiFile(): Write a Usagi mapping file