omopgenerics
Methods and Classes for the OMOP Common Data Model

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omopgenerics: Methods and Classes for the OMOP Common Data Model
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API for omopgenerics
Methods and Classes for the OMOP Common Data Model

Global functions
$.cdm_reference Man page
$<-.cdm_reference Man page
.validateAchillesTable Source code
.validateOmopTable Source code
[[.cdm_reference Man page
[[<-.cdm_reference Man page
`$.cdm_reference` Source code
`$<-.cdm_reference` Source code
`[.codelist_with_details` Source code
`[.codelist` Source code
`[.concept_set_expression` Source code
`[[.cdm_reference` Source code
`[[<-.cdm_reference` Source code
`cdmName<-.cdm_reference` Source code
`cdmName<-` Source code
abortReadOnlySource Source code
achillesColumns Man page Source code
achillesTables Man page Source code
addClass Source code
addLabels Source code
addMesSup Source code
addPkgDetails Source code
addSettings Man page Source code
addSignal Source code
additionalColumns Man page Source code
anti_join.cdm_table Source code
appendNoNa Source code
arrange.cdm_table Source code
as_tibble.codelist Source code
as_tibble.codelist_with_details Source code
as_tibble.concept_set_expression Source code
assertCharacter Man page Source code
assertChoice Man page Source code
assertClass Man page Source code
assertClassification Source code
assertDate Man page Source code
assertDoc Man page
assertList Man page Source code
assertLogical Man page Source code
assertNumeric Man page Source code
assertTable Man page Source code
assertTableName Source code
assertTrue Man page Source code
assertValidation Source code
assertVersion Source code
assertWindowName Source code
attrition Man page Source code
attrition.cohort_table Man page Source code
bind Man page Source code
bind.NULL Source code
bind.codelist Source code
bind.codelist_with_details Source code
bind.cohort_table Man page Source code
bind.concept_set_expression Source code
bind.list Source code
bind.summarised_result Man page Source code
c.codelist Source code
c.codelist_with_details Source code
c.concept_set_expression Source code
castAchillesColumns Source code
castCodeSearchColumns Source code
castCohortColumns Source code
castColumns Source code
castDoc Man page
castOmopColumns Source code
castTableColumns Source code
cdi Source code
cdmAssignTableDoc Man page
cdmClasses Man page Source code
cdmDisconnect Man page Source code
cdmDisconnect.cdm_reference Source code
cdmDisconnect.local_cdm Source code
cdmDisconnect.read_only_source Source code
cdmDoc Man page
cdmFromTables Man page Source code
cdmIndexDoc Man page
cdmName Man page Source code
cdmName.cdm_reference Source code
cdmName.cdm_table Source code
cdmName.default Source code
cdmName<- Man page
cdmNameDoc Man page
cdmOrTableDoc Man page
cdmReference Man page Source code
cdmSelect Man page Source code
cdmSource Man page Source code
cdmSource.cdm_reference Source code
cdmSource.cdm_table Source code
cdmSource.default Source code
cdmSourceType Man page Source code
cdmTableDoc Man page
cdmTableFromSource Man page Source code
cdmTableFromSource.local_cdm Source code
cdmTableFromSource.read_only_source Source code
cdmVersion Man page Source code
cdmVersion.cdm_reference Source code
cdmVersion.cdm_table Source code
cdmVersion.default Source code
cdmVersionArgumentDoc Man page
checkChoices Source code
checkClass Source code
checkCodelistInConcept Source code
checkCodelistType Source code
checkCohortAttributes Source code
checkCohortRequirements Man page Source code
checkColumnContent Source code
checkColumns Source code
checkColumns2 Source code
checkColumnsCdm Source code
checkColumnsFormat Source code
checkDistinct Source code
checkDuplicated Source code
checkEmpty Source code
checkFunction Source code
checkGroupCount Source code
checkInherits Source code
checkIntegerish Source code
checkLength Source code
checkListClass Source code
checkMax Source code
checkMin Source code
checkMinCharacter Source code
checkNA Source code
checkNa Source code
checkNaCohort Source code
checkNamed Source code
checkNull Source code
checkNumberColumns Source code
checkNumberRows Source code
checkNumeric Source code
checkObservationPeriod Source code
checkOverlap Source code
checkOverlapObservation Source code
checkPerson Source code
checkPivotEstimatesBy Source code
checkPlausibleObservationDates Source code
checkSettingsColumns Source code
checkStartBeforeEndObservation Source code
checkStartEnd Source code
checkTrue Source code
checkUnique Source code
cl Source code
cliCallDoc Man page
codelistDoc Man page
codelistWithDetailsDoc Man page
cohortAttibutesSuffixes Source code
cohortCodelist Man page Source code
cohortColumns Man page Source code
cohortCount Man page Source code
cohortDoc Man page
cohortTables Man page Source code
cohortValidationChecksDoc Man page
collapse.cdm_table Source code
collapseStr Source code
collect.cdm_reference Man page Source code
collect.cdm_table Source code
collect.cohort_table Man page Source code
combine Source code
combineCodelist Source code
combineStrata Man page Source code
compareOmopTableFields Man page Source code
compute.cdm_table Man page Source code
compute.local_cdm Source code
compute.read_only_source Source code
conceptCdmDoc Man page
conceptSetExpressionDoc Man page
consistentNaming Source code
constructCdmReference Source code
constructCdmSource Source code
constructCodelist Source code
constructCodelistWithDetails Source code
constructConceptSetExpression Source code
constructGeneratedCohortSet Source code
constructSummarisedResult Source code
correctAgeGroup Source code
count.cdm_table Source code
createCheckObject Source code
createIndexes Man page Source code
createLogFile Man page Source code
createLogger Source code
createSettings Source code
createTableIndex Man page Source code
createTableIndex.cdm_table Source code
createTableIndex.default Source code
cross_join.cdm_table Source code
dateOpt Source code
decodeNa Source code
defaultCohortAttrition Source code
defaultCohortCodelist Source code
defaultCohortSet Source code
detectColsToCast Source code
distinct.cdm_table Source code
dropSourceTable Man page Source code
dropSourceTable.cdm_reference Source code
dropSourceTable.cdm_table Source code
dropSourceTable.local_cdm Source code
dropSourceTable.read_only_source Source code
dropTable Man page Source code
emptyAchillesTable Man page Source code
emptyCdmReference Man page Source code
emptyCodeSearch Man page Source code
emptyCodelist Man page Source code
emptyCodelistWithDetails Man page Source code
emptyCohortTable Man page Source code
emptyConceptSetExpression Man page Source code
emptyDoc Man page
emptyOmopTable Man page Source code
emptyOmopTableInternal Source code
emptySummarisedResult Man page Source code
emptyTable Source code
emptyTableNameDoc Man page
encodeNa Source code
equal Source code
errorMessage Source code
estimateTypeChoices Man page Source code
existingIndexes Man page Source code
existingIndexes.cdm_reference Source code
existingIndexes.cdm_table Source code
existingIndexes.default Source code
expectedIndexes Man page Source code
expectedIndexes.cdm_reference Source code
expectedIndexes.cdm_table Source code
expectedIndexes.default Source code
exportCodeSearch Man page Source code
exportCodelist Man page Source code
exportCodelistWithDetails Man page Source code
exportConceptSetExpression Man page Source code
exportFileDoc Man page
exportSummarisedResult Man page Source code
extractColumns Source code
filter Man page
filter.cdm_table Source code
filterAdditional Man page Source code
filterGroup Man page Source code
filterNameLevel Source code
filterResult Man page Source code
filterResultCall Source code
filterResultExpression Source code
filterResultInform Source code
filterResultNameLevelColumns Source code
filterResultResult Source code
filterResultSplitAnd Source code
filterResultVariables Source code
filterResultWarnEmpty Source code
filterResultWhere Source code
filterSettings Man page Source code
filterStrata Man page Source code
findFiles Source code
findNewName Source code
finishLogQuery Source code
formatExplain Source code
formatQuery Source code
full_join.cdm_table Source code
funToCast Source code
getCohortId Man page Source code
getCohortName Man page Source code
getColumns Source code
getEmptyField Source code
getFields Source code
getFormat Source code
getGrouping Source code
getLabels Source code
getLevels Source code
getPersonIdentifier Man page Source code
getType Source code
getTypes Source code
getVersion Source code
getVocabularyVersion Source code
getWindowNames Source code
giveType Source code
groupColumns Man page Source code
group_by.cdm_table Source code
identical_type_insensitive Source code
importCodeSearch Man page Source code
importCodelist Man page Source code
importCodelistWithDetails Man page Source code
importConceptSetExpression Man page Source code
importFileDoc Man page
importSummarisedResult Man page Source code
increaseQueryId Source code
inner_join.cdm_table Source code
insertCdmTo Man page Source code
insertCdmTo.cdm_reference Source code
insertCdmTo.local_cdm Source code
insertCdmTo.read_only_source Source code
insertFromSource Man page Source code
insertFromSource.local_cdm Source code
insertFromSource.read_only_source Source code
insertRef Source code
insertTable Man page Source code
insertTable.cdm_reference Source code
insertTable.cdm_table Source code
insertTable.local_cdm Source code
insertTable.read_only_source Source code
intersect.cdm_table Source code
invertChanges Source code
isCase Source code
isIntegerish Source code
isNegatedSelection Source code
isResultSuppressed Man page Source code
isSentenceCase Source code
isSnakeCase Source code
isTableEmpty Man page Source code
joinCohortNameFromSettings Source code
keepAttributes Source code
keepClass Source code
left_join.cdm_table Source code
listSourceTables Man page Source code
listSourceTables.cdm_reference Source code
listSourceTables.cdm_table Source code
listSourceTables.local_cdm Source code
listSourceTables.read_only_source Source code
logMessage Man page Source code
metadata Source code
missingCohortTableNameError Source code
missingColumns Source code
mutate.cdm_table Source code
naValue Source code
nameAgeGroup Source code
nameBullet Source code
nameConceptSet Source code
nameLevel Source code
nameLevelColumns Source code
nameLevelSeparator Source code
nest_join.cdm_table Source code
newAchillesTable Man page Source code
newCdmReference Man page Source code
newCdmSource Man page Source code
newCdmTable Man page Source code
newCodeSearch Man page Source code
newCodelist Man page Source code
newCodelistWithDetails Man page Source code
newCohortTable Man page Source code
newConceptSetExpression Man page Source code
newLocalSource Man page Source code
newNameLevel Source code
newOmopTable Man page Source code
newReadOnlySource Man page Source code
newSummarisedResult Man page Source code
noReference Source code
numberRecords Man page Source code
numberSubjects Man page Source code
objectLength Source code
omopCdmVersionDoc Man page
omopColumns Man page Source code
omopDataFolder Man page Source code
omopTableFields Man page Source code
omopTables Man page Source code
omopgenerics Man page
omopgenerics-package Man page
overwriteDoc Man page
pivotEstimates Man page Source code
pivotSettings Source code
pivot_longer.cdm_table Source code
pivot_wider.cdm_table Source code
plural Source code
populateCohortAttrition Source code
populateCohortCodelist Source code
populateCohortSet Source code
prepareResult Source code
print.cdm_reference Man page Source code
print.cdm_source Source code
print.cdm_source_summary Source code
print.code_search Man page Source code
print.codelist Man page Source code
print.codelist_with_details Man page Source code
print.compare_table_fields Source code
print.conceptSetExpression Source code
print.concept_set_expression Man page Source code
queryFile Source code
queryId Source code
readConceptSetExpression Source code
readSourceTable Man page Source code
readSourceTable.cdm_reference Source code
readSourceTable.cdm_table Source code
readSourceTable.read_only_source Source code
recordCohortAttrition Man page Source code
recursiveDoc Man page
reexports Man page
removeClass Source code
removeRepeated Source code
rename.cdm_table Source code
renameCodelists Source code
report Source code
reportIndex Source code
reportOverlap Source code
restoreAttributes Source code
restoreClass Source code
resultColumns Man page Source code
resultPackageVersion Man page Source code
resultType Man page Source code
resultType.NULL Source code
resultType.character Source code
resultType.omopgenerics Source code
right_join.cdm_table Source code
rowwise.cdm_table Source code
searchStrategy Man page Source code
select.cdm_table Source code
selectType Source code
semi_join.cdm_table Source code
settings Man page Source code
settings.cohort_table Man page Source code
settings.summarised_result Man page Source code
settingsColumns Man page Source code
slice.cdm_table Source code
slice_head.cdm_table Source code
slice_max.cdm_table Source code
slice_min.cdm_table Source code
slice_sample.cdm_table Source code
slice_tail.cdm_table Source code
sourceType Man page Source code
sourceType.cdm_reference Source code
sourceType.cdm_source Source code
sourceType.cdm_table Source code
sourceType.default Source code
splitAdditional Man page Source code
splitAll Man page Source code
splitGroup Man page Source code
splitNameLevelInternal Source code
splitNameLevelText Source code
splitStrata Man page Source code
startLogQuery Source code
statusIndexes Man page Source code
str.cdm_reference Source code
strataColumns Man page Source code
summarise.cdm_table Source code
summariseLogFile Man page Source code
summariseLogSqlPath Source code
summarisedResultDoc Man page
summary.cdm_reference Man page Source code
summary.cdm_source Man page Source code
summary.cohort_table Man page Source code
summary.local_cdm Source code
summary.read_only_source Source code
summary.summarised_result Man page Source code
suppress Man page Source code
suppress.summarised_result Man page Source code
suppressColumn Source code
suppressCounts Source code
suppressGroup Source code
suppressLinkage Source code
suppressVariable Source code
tableChoice Source code
tableName Man page Source code
tableSource Man page Source code
tally.cdm_table Source code
thereIsOverlap Source code
tidy Man page
tidy.summarised_result Man page Source code
tidyColumns Man page Source code
tidySelect Source code
tmpPrefix Man page Source code
toSnakeCase Man page Source code
transformToSummarisedResult Man page Source code
ungroup.cdm_table Source code
union.cdm_table Source code
unionCohorts Source code
union_all.cdm_table Source code
uniqueCols Source code
uniqueId Man page Source code
uniqueTableName Man page Source code
uniteAdditional Man page Source code
uniteGroup Man page Source code
uniteNameLevelInternal Source code
uniteStrata Man page Source code
unusedDotsDoc Man page
updateAttrition Source code
updateCohortNames Source code
validateAchillesTable Man page Source code
validateAgeGroupArgument Man page Source code
validateCdmArgument Man page Source code
validateCdmReference Source code
validateCdmSource Source code
validateCdmTable Man page Source code
validateCodeSearch Source code
validateCodelist Source code
validateCodelistWithDetails Source code
validateCohortArgument Man page Source code
validateCohortIdArgument Man page Source code
validateColumn Man page Source code
validateConceptSetArgument Man page Source code
validateConceptSetExpression Source code
validateDates Source code
validateGeneratedCohortSet Source code
validateName Source code
validateNameArgument Man page Source code
validateNameLevel Man page Source code
validateNameStyle Man page Source code
validateNewColumn Man page Source code
validateOmopTable Man page Source code
validateResultArgument Man page Source code
validateResultSettings Source code
validateStrataArgument Man page Source code
validateSummarisedResult Source code
validateSummarisedResultTable Source code
validateTidyNames Source code
validateWindowArgument Man page Source code
validateX Source code
validationDoc Man page
variableTypes Source code
verb Source code
warnColsToCast Source code
writeChanges Source code
writeCodelist Source code
writeCodelistWithDetails Source code
writeConceptSetExpression Source code
writeMessage Source code
omopgenerics documentation built on June 17, 2026, 5:07 p.m.

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