Function reference • omopgenerics

All functions

achillesColumns(): Required columns for each of the achilles result tables

achillesTables(): Names of the tables that contain the results of achilles analyses

attrition(): Get attrition from an object.

attrition(<cohort_table>): Get cohort attrition from a cohort_table object.

bind(): Bind two or more objects of the same class.

bind(<cohort_table>): Bind two or more cohort tables

bind(<summarised_result>): Bind two or summarised_result objects

`$`(<cdm_reference>): Subset a cdm reference object.

`$<-`(<cdm_reference>): Assign an table to a cdm reference.

cdmFromTables(): Create a cdm object from local tables

cdmName(): Get the name of a cdm_reference associated object

cdmReference(): Get the cdm_reference of a cdm_table.

cdmSelect(): Restrict the cdm object to a subset of tables.

cdmSource(): Get the source of a cdm_reference.

cdmSourceType(): Get the source type of a cdm_reference object.

cdmTableFromSource(): This is an internal developer focused function that creates a cdm_table from a table that shares the source but it is not a cdm_table. Please use insertTable if you want to insert a table to a cdm_reference object.

cdmVersion(): Get the version of a cdm_reference.

checkCohortRequirements(): Check whether a cohort table satisfies requirements

cohortCodelist(): Get codelist from a cohort_table object.

cohortColumns(): Required columns for a generated cohort set.

cohortCount(): Get cohort counts from a cohort_table object.

cohortTables(): Cohort tables that a cdm reference can contain in the OMOP Common Data Model.

collect(<cdm_reference>): Retrieves the cdm reference into a local cdm.

collect(<cohort_table>): To collect a cohort_table object.

compute(<cdm_table>): Store results in a table.

dropSourceTable(): Drop a table from a cdm object.

dropTable(): Drop a table from a cdm object.

emptyAchillesTable(): Create an empty achilles table

emptyCdmReference(): Create an empty cdm_reference

emptyCodelist(): Empty codelist object.

emptyCohortTable(): Create an empty cohort_table object

emptyOmopTable(): Create an empty omop table

emptySummarisedResult(): Empty summarised_result object.

estimateTypeChoices(): Choices that can be present in estimate_type column.

exportSummarisedResult(): Export a summarised_result object to a csv file.

getCohortId(): Get the cohort definition id of a certain name

getCohortName(): Get the cohort name of a certain cohort definition id

insertFromSource(): Convert a table that is not a cdm_table but have the same original source to a cdm_table. This Table is not meant to be used to insert tables in the cdm, please use insertTable instead.

insertTable(): Insert a table to a cdm object.

listSourceTables(): List tables that can be accessed though a cdm object.

newAchillesTable(): Create an achilles table from a cdm_table.

newCdmReference(): cdm_reference objects constructor

newCdmSource(): Create a cdm source object.

newCdmTable(): Create an cdm table.

newCodelist(): 'codelist' object constructor

newCohortTable(): cohort_table objects constructor.

newConceptSetExpression(): 'conceptSetExpression' object constructor

newLocalSource(): A new local source for the cdm

newOmopTable(): Create an omop table from a cdm table.

newSummarisedResult(): 'summarised_results' object constructor

omopColumns(): Required columns that the standard tables in the OMOP Common Data Model must have.

omopTables(): Standard tables that a cdm reference can contain in the OMOP Common Data Model.

participants(): It returns the participants that contributed to a particular analysis

print(<cdm_reference>): Print a CDM reference object

print(<codelist>): Print a codelist

print(<conceptSetExpression>): Print a concept set expression

readSourceTable(): Read a table from the cdm_source and add it to to the cdm.

recordCohortAttrition(): Update cohort attrition.

resultColumns(): Required columns that the result tables must have.

settings(): Get settings from an object.

settings(<cohort_table>): Get cohort settings from a cohort_table object.

settings(<summarised_result>): Get settings from a summarised_result object.

sourceType(): Get the source type of a cdm_source.

`[[`(<cdm_reference>): Subset a cdm reference object.

`[[<-`(<cdm_reference>): Assign a table to a cdm reference.

summary(<cdm_reference>): Summary a cdm reference

summary(<cohort_table>): Summary a generated cohort set

summary(<summarised_result>): Summary a summarised_result

suppress(): Function to suppress counts in result objects

suppress(<summarised_result>): Function to suppress counts in result objects

tableName(): Get the table name of a cdm_table.

tableSource(): Get the table source of a cdm_table.

tmpPrefix(): Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.

toSnakeCase(): Convert a character vector to snake case

uniqueTableName(): Create a unique table name

validateNameLevel(): Validate if two columns are valid Name-Level pair.