Methods and Classes for the OMOP Common Data Model

Documentation for package ‘omopgenerics’ version 0.3.0

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-- A --

achillesColumns	Required columns for each of the achilles result tables
achillesTables	Names of the tables that contain the results of achilles analyses
assertCharacter	Assert that an object is a character and fulfill certain conditions.
assertChoice	Assert that an object is within a certain oprtions.
assertClass	Assert that an object has a certain class.
assertDate	Assert Date
assertList	Assert that an object is a list.
assertLogical	Assert that an object is a logical.
assertNumeric	Assert that an object is a numeric.
assertTable	Assert that an object is a table.
assertTrue	Assert that an expression is TRUE.
attrition	Get attrition from an object.
attrition.cohort_table	Get cohort attrition from a cohort_table object.

-- B --

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

-- C --

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 cdmSource of an object.
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 an object.
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.

-- D --

dropSourceTable	Drop a table from a cdm object.
dropTable	Drop a table from a cdm object.

-- E --

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.
exportCodelist	Export a codelist object.
exportConceptSetExpression	Export a concept set expression.
exportSummarisedResult	Export a summarised_result object to a csv file.

-- G --

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.

-- I --

importCodelist	Import a codelist.
importConceptSetExpression	Import a concept set expression.
importSummarisedResult	Import a set of summarised results.
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.

-- L --

List tables that can be accessed though a cdm object.

-- N --

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

-- O --

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.

-- P --

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

-- R --

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.

-- S --

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 an object.
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

-- T --

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

-- U --

uniqueId	Get a unique Identifier with a certain number of characters and a prefix.
uniqueTableName	Create a unique table name

-- V --

validateAgeGroupArgument	validateAgeGroupArgument
validateCdmArgument	validateCdmArgument
validateCohortArgument	Validate a cohort table input.
validateCohortIdArgument	Validate cohortId argument.
validateConceptSetArgument	Validate conceptSet argument.
validateNameArgument	Validate name argument.
validateNameLevel	Validate if two columns are valid Name-Level pair.
validateResultArguemnt	validateResultArguemnt
validateWindowArgument	validateWindowArgument

-- misc --

$.cdm_reference	Subset a cdm reference object.
$<-.cdm_reference	Assign an table to a cdm reference.
[[.cdm_reference	Subset a cdm reference object.
[[<-.cdm_reference	Assign a table to a cdm reference.