Methods and Classes for the OMOP Common Data Model

Documentation for package ‘omopgenerics’ version 1.1.0

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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
additionalColumns	Identify variables in additional_name column
addSettings	Add settings columns to a <summarised_result> object
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 --

cdmDisconnect	Disconnect from a cdm object.
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.
combineStrata	Provide all combinations of strata levels.
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. [Deprecated]

-- 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.

-- F --

filterAdditional	Filter the additional_name-additional_level pair in a summarised_result
filterGroup	Filter the group_name-group_level pair in a summarised_result
filterSettings	Filter a <summarised_result> using the settings
filterStrata	Filter the strata_name-strata_level pair in a summarised_result

-- 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.
groupColumns	Identify variables in group_name column

-- I --

importCodelist	Import a codelist.
importConceptSetExpression	Import a concept set expression.
importSummarisedResult	Import a set of summarised results.
insertCdmTo	Insert a cdm_reference object to a different source.
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.
isResultSuppressed	To check whether an object is already suppressed to a certain min cell count.
isTableEmpty	Check if a table is empty or not

-- L --

listSourceTables

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
numberRecords	Count the number of records that a 'cdm_table' has.
numberSubjects	Count the number of subjects that a 'cdm_table' has.

-- O --

omopColumns	Required columns that the standard tables in the OMOP Common Data Model must have.
omopTableFields	Return a table of omop cdm fields informations
omopTables	Standard tables that a cdm reference can contain in the OMOP Common Data Model.

-- P --

pivotEstimates	Set estimates as columns
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.
resultPackageVersion	Check if different packages version are used for summarise_results object

-- 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.
settingsColumns	Identify settings columns of a <summarised_result>
sourceType	Get the source type of an object.
splitAdditional	Split additional_name and additional_level columns
splitAll	Split all pairs name-level into columns.
splitGroup	Split group_name and group_level columns
splitStrata	Split strata_name and strata_level columns
strataColumns	Identify variables in strata_name column
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'.
tidy.summarised_result	Turn a <summarised_result> object into a tidy tibble
tidyColumns	Identify tidy columns of a <summarised_result>
tmpPrefix	Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.
toSnakeCase	Convert a character vector to snake case
transformToSummarisedResult	Create a <summarised_result> object from a data.frame, given a set of specifications.

-- U --

uniqueId	Get a unique Identifier with a certain number of characters and a prefix.
uniqueTableName	Create a unique table name
uniteAdditional	Unite one or more columns in additional_name-additional_level format
uniteGroup	Unite one or more columns in group_name-group_level format
uniteStrata	Unite one or more columns in strata_name-strata_level format

-- V --

validateAchillesTable	Validate if a cdm_table is a valid achilles table.
validateAgeGroupArgument	Validate the ageGroup argument. It must be a list of two integerish numbers lower age and upper age, both of the must be greater or equal to 0 and lower age must be lower or equal to the upper age. If not named automatic names will be given in the output list.
validateCdmArgument	Validate if an object in a valid cdm_reference.
validateCdmTable	Validate if a table is a valid cdm_table object.
validateCohortArgument	Validate a cohort table input.
validateCohortIdArgument	Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referinc to cohort_names. If you want to support tidyselect expressions please use the function as: 'validateCohortIdArgument({{cohortId}}, cohort)'.
validateColumn	Validate whether a variable points to a certain exiting column in a table.
validateConceptSetArgument	Validate conceptSet argument. It can either be a list, a codelist, a conceptSetExpression or a codelist with details. The output will always be a codelist.
validateNameArgument	Validate name argument. It must be a snake_case character vector. You can add the a cdm object to check 'name' is not already used in that cdm.
validateNameLevel	Validate if two columns are valid Name-Level pair.
validateNameStyle	Validate 'nameStyle' argument. If any of the element in '...' has length greater than 1 it must be contained in nameStyle. Note that snake case notation is used.
validateNewColumn	Validate a new column of a table
validateOmopTable	Validate an omop_table
validateResultArgument	Validate if a an object is a valid 'summarised_result' object.
validateStrataArgument	To validate a strata list. It makes sure that elements are unique and point to columns in table.
validateWindowArgument	Validate a window argument. It must be a list of two elements (window start and window end), both must be integerish and window start must be lower or equal than window end.

-- 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.