Methods and Classes for the OMOP Common Data Model

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Documentation for package ‘omopgenerics’ version 0.2.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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$.cdm_reference	Subset a cdm reference object.
$<-.cdm_reference	Assign an table to a cdm reference.
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
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.
emptyCodelistWithDetails	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
getPersonIdentifier	Get the column name with the person identifier from a table (either subject_id or person_id), it will throw an error if it contains both or neither.
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
newCodelistWithDetails	'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.codelist_with_details	Print a codelist with details
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.
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
uniqueId	Get a unique Identifier with a certain number of characters and a prefix.
uniqueTableName	Create a unique table name
validateNameLevel	Validate if two columns are valid Name-Level pair.
[[.cdm_reference	Subset a cdm reference object.
[[<-.cdm_reference	Assign a table to a cdm reference.