Man pages for omopgenerics
Methods and Classes for the OMOP Common Data Model

achillesColumnsRequired columns for each of the achilles result tables
achillesTablesNames of the tables that contain the results of achilles...
assertCharacterAssert that an object is a character and fulfill certain...
assertChoiceAssert that an object is within a certain oprtions.
assertClassAssert that an object has a certain class.
assertDateAssert Date
assertListAssert that an object is a list.
assertLogicalAssert that an object is a logical.
assertNumericAssert that an object is a numeric.
assertTableAssert that an object is a table.
assertTrueAssert that an expression is TRUE.
attritionGet attrition from an object.
attrition.cohort_tableGet cohort attrition from a cohort_table object.
bindBind two or more objects of the same class.
bind.cohort_tableBind two or more cohort tables
bind.summarised_resultBind two or summarised_result objects
cash-.cdm_referenceSubset a cdm reference object.
cash-set-.cdm_referenceAssign an table to a cdm reference.
cdmFromTablesCreate a cdm object from local tables
cdmNameGet the name of a cdm_reference associated object
cdmReferenceGet the 'cdm_reference' of a 'cdm_table'.
cdmSelectRestrict the cdm object to a subset of tables.
cdmSourceGet the cdmSource of an object.
cdmSourceTypeGet the source type of a cdm_reference object.
cdmTableFromSourceThis is an internal developer focused function that creates a...
cdmVersionGet the version of an object.
checkCohortRequirementsCheck whether a cohort table satisfies requirements
cohortCodelistGet codelist from a cohort_table object.
cohortColumnsRequired columns for a generated cohort set.
cohortCountGet cohort counts from a cohort_table object.
cohortTablesCohort tables that a cdm reference can contain in the OMOP...
collect.cdm_referenceRetrieves the cdm reference into a local cdm.
collect.cohort_tableTo collect a 'cohort_table' object.
combineStrataProvide all combinations of strata levels.
compute.cdm_tableStore results in a table.
dropSourceTableDrop a table from a cdm object.
dropTableDrop a table from a cdm object.
emptyAchillesTableCreate an empty achilles table
emptyCdmReferenceCreate an empty cdm_reference
emptyCodelistEmpty 'codelist' object.
emptyCodelistWithDetailsEmpty 'codelist' object.
emptyCohortTableCreate an empty cohort_table object
emptyOmopTableCreate an empty omop table
emptySummarisedResultEmpty 'summarised_result' object.
estimateTypeChoicesChoices that can be present in 'estimate_type' column.
exportCodelistExport a codelist object.
exportConceptSetExpressionExport a concept set expression.
exportSummarisedResultExport a summarised_result object to a csv file.
getCohortIdGet the cohort definition id of a certain name
getCohortNameGet the cohort name of a certain cohort definition id
getPersonIdentifierGet the column name with the person identifier from a table...
importCodelistImport a codelist.
importConceptSetExpressionImport a concept set expression.
importSummarisedResultImport a set of summarised results.
insertFromSourceConvert a table that is not a cdm_table but have the same...
insertTableInsert a table to a cdm object.
isResultSuppressedisResultSuppressed
isTableEmptyCheck if a table is empty or not
listSourceTablesList tables that can be accessed though a cdm object.
newAchillesTableCreate an achilles table from a cdm_table.
newCdmReference'cdm_reference' objects constructor
newCdmSourceCreate a cdm source object.
newCdmTableCreate an cdm table.
newCodelist'codelist' object constructor
newCodelistWithDetails'codelist' object constructor
newCohortTable'cohort_table' objects constructor.
newConceptSetExpression'conceptSetExpression' object constructor
newLocalSourceA new local source for the cdm
newOmopTableCreate an omop table from a cdm table.
newSummarisedResult'summarised_results' object constructor
omopColumnsRequired columns that the standard tables in the OMOP Common...
omopgenerics-packageomopgenerics: Methods and Classes for the OMOP Common Data...
omopTableFieldsReturn a table of omop cdm fields informations
omopTablesStandard tables that a cdm reference can contain in the OMOP...
participantsIt returns the participants that contributed to a particular...
print.cdm_referencePrint a CDM reference object
print.codelistPrint a codelist
print.codelist_with_detailsPrint a codelist with details
print.conceptSetExpressionPrint a concept set expression
readSourceTableRead a table from the cdm_source and add it to to the cdm.
recordCohortAttritionUpdate cohort attrition.
reexportsObjects exported from other packages
resultColumnsRequired columns that the result tables must have.
resultPackageVersionCheck if different packages version are used for...
settingsGet settings from an object.
settings.cohort_tableGet cohort settings from a cohort_table object.
settings.summarised_resultGet settings from a summarised_result object.
sourceTypeGet the source type of an object.
sub-sub-.cdm_referenceSubset a cdm reference object.
sub-subset-.cdm_referenceAssign a table to a cdm reference.
summary.cdm_referenceSummary a cdm reference
summary.cohort_tableSummary a generated cohort set
summary.summarised_resultSummary a summarised_result
suppressFunction to suppress counts in result objects
suppress.summarised_resultFunction to suppress counts in result objects
tableNameGet the table name of a 'cdm_table'.
tableSourceGet the table source of a 'cdm_table'.
tmpPrefixCreate a temporary prefix for tables, that contains a unique...
toSnakeCaseConvert a character vector to snake case
uniqueIdGet a unique Identifier with a certain number of characters...
uniqueTableNameCreate a unique table name
validateAgeGroupArgumentvalidateAgeGroupArgument
validateCdmArgumentvalidateCdmArgument
validateCohortArgumentValidate a cohort table input.
validateCohortIdArgumentValidate cohortId argument.
validateConceptSetArgumentValidate conceptSet argument.
validateNameArgumentValidate name argument.
validateNameLevelValidate if two columns are valid Name-Level pair.
validateResultArguemntvalidateResultArgument
validateResultArgumentvalidateResultArgument
validateWindowArgumentvalidateWindowArgument
omopgenerics documentation built on Sept. 30, 2024, 9:16 a.m.