R: Methods and Classes for the OMOP Common Data Model

# Methods and Classes for the OMOP Common Data Model

## Documentation for package ‘omopgenerics’ version 1.3.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L N O P R S T U V misc

## -- 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 --

cdmClasses | Separate the cdm tables in classes
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.
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.
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.
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.
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
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.
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.
omopDataFolder | Check or set the OMOP_DATA_FOLDER where the OMOP related data is stored.
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.concept_set_expression | 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
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 | Summary a cdm reference
summary.cdm_source | Summarise a 'cdm_source' object
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 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 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.