Methods and Classes for the OMOP Common Data Model

Documentation for package ‘omopgenerics’ version 1.4.0

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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 satisfies certain conditions.
assertChoice	Assert that an object is one of a set of options.
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 --

cdmClasses	Separate the cdm tables in classes
cdmDisconnect	Disconnect from a cdm object.
cdmFromTables	Create a cdm object from local tables
cdmName	Get or set the name of a cdm_reference associated object
cdmName<-	Get or set 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	Retrieve the cdm reference into a local cdm.
collect.cohort_table	To collect a 'cohort_table' object.
combineStrata	Provide all combinations of strata levels.
compareOmopTableFields	Compare the fields of two different OMOP CDM versions
compute.cdm_table	Store results in a table.
createIndexes	Create the missing indexes
createLogFile	Create a log file
createTableIndex	Create a table index

-- 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.
emptyCodeSearch	Empty code search object
emptyCohortTable	Create an empty cohort_table object
emptyConceptSetExpression	Empty 'concept_set_expression' object.
emptyOmopTable	Create an empty omop table
emptySummarisedResult	Empty 'summarised_result' object.
estimateTypeChoices	Choices that can be present in 'estimate_type' column.
existingIndexes	Existing indexes in a cdm object
expectedIndexes	Expected indexes in a cdm object
exportCodelist	Export a codelist object.
exportCodelistWithDetails	Export a codelist with details object.
exportCodeSearch	Export a 'code_search' object into an Excel spreadsheet
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
filterResult	Filter a <summarised_result> automatically
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.
importCodelistWithDetails	Import a codelist with details.
importCodeSearch	Import a 'code_search' object from an Excel spreadsheet
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 into 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 through a cdm object.
logMessage	Log a message to a logFile

-- 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
newCodeSearch	Create a new 'code_search' object
newCohortTable	'cohort_table' objects constructor.
newConceptSetExpression	'concept_set_expression' object constructor
newLocalSource	A new local source for the cdm
newOmopTable	Create an omop table from a cdm table.
newReadOnlySource	A new read-only source for the cdm
newSummarisedResult	'summarised_result' 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.
omopDataFolder	Check or set the OMOP_DATA_FOLDER where the OMOP related data is stored.
omopTableFields	Return a table of omop cdm field information
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.code_search	Print a code search
print.concept_set_expression	Print a concept set expression

-- R --

readSourceTable	Read a table from the cdm_source and add it to the cdm.
recordCohortAttrition	Update cohort attrition.
resultColumns	Required columns that the result tables must have.
resultPackageVersion	Check if different package versions are used for a summarised_result object
resultType	Get the 'result_type(s)' defined in a certain package

-- S --

searchStrategy	Get the search strategy used to create a 'code_search'
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
statusIndexes	Status of the indexes
strataColumns	Identify variables in strata_name column
summariseLogFile	Summarise and extract the information of a log file into a 'summarised_result' object.
summary.cdm_reference	Summarise a cdm reference
summary.cdm_source	Summarise a 'cdm_source' object
summary.cohort_table	Summarise a generated cohort set
summary.summarised_result	Summarise 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 referring 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 existing column in a table.
validateConceptSetArgument	Validate conceptSet argument. It can either be a list, a codelist, a concept set expression 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 a cdm object to check that '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 whether 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 numeric, integerish by default, and window start must be lower or equal than window end.

-- misc --

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