Package index • omopgenerics

Methods

General methods deffined by omopgenerics

attrition(): Get attrition from an object.

bind(): Bind two or more objects of the same class.

settings(): Get settings from an object.

suppress(): Function to suppress counts in result objects

Create new objects

To create new omopgenerics S3 classes objects

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

Creates empty objects

To create empty omopgenerics S3 classes objects

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.

cdm_reference utility functions

Utility functions for cdm_reference objects

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() deprecated: 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.

listSourceTables(): List tables that can be accessed though a cdm object.

dropSourceTable(): Drop a table from a cdm object.

insertTable(): Insert a table to a cdm object.

readSourceTable(): Read a table from the cdm_source and add it to to the cdm.

insertCdmTo(): Insert a cdm_reference object to a different source.

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.

`$`(<cdm_reference>): Subset a cdm reference object.

`$<-`(<cdm_reference>): Assign an table to a cdm reference.

collect(<cdm_reference>): Retrieves the cdm reference into a local cdm.

print(<cdm_reference>): Print a CDM reference object

`[[`(<cdm_reference>): Subset a cdm reference object.

`[[<-`(<cdm_reference>): Assign a table to a cdm reference.

summary(<cdm_reference>): Summary a cdm reference

summary(<cdm_source>): Summarise a cdm_source object

cdm_table utility functions

Utility functions for cdm_table objects

tableName(): Get the table name of a cdm_table.

tableSource(): Get the table source of a cdm_table.

numberRecords(): Count the number of records that a cdm_table has.

numberSubjects(): Count the number of subjects that a cdm_table has.

compute(<cdm_table>): Store results in a table.

omop_table utility functions

Utility functions for omop_table objects

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.

achilles_table utility functions

Utility functions for achilles_table objects

achillesColumns(): Required columns for each of the achilles result tables

achillesTables(): Names of the tables that contain the results of achilles analyses

cohort_table utility functions

Utility functions for cohort_table objects

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.

getCohortId(): Get the cohort definition id of a certain name

getCohortName(): Get the cohort name of a certain cohort definition id

recordCohortAttrition(): Update cohort attrition.

attrition(<cohort_table>): Get cohort attrition from a cohort_table object.

bind(<cohort_table>): Bind two or more cohort tables

collect(<cohort_table>): To collect a cohort_table object.

settings(<cohort_table>): Get cohort settings from a cohort_table object.

summary(<cohort_table>): Summary a generated cohort set

summarised_result utility functions

Utility functions for summarised_result objects

transformToSummarisedResult(): Create a <summarised_result> object from a data.frame, given a set of specifications.

exportSummarisedResult(): Export a summarised_result object to a csv file.

importSummarisedResult(): Import a set of summarised results.

estimateTypeChoices(): Choices that can be present in estimate_type column.

resultColumns(): Required columns that the result tables must have.

resultPackageVersion(): Check if different packages version are used for summarise_results object

isResultSuppressed(): To check whether an object is already suppressed to a certain min cell count.

bind(<summarised_result>): Bind two or summarised_result objects

settings(<summarised_result>): Get settings from a summarised_result object.

summary(<summarised_result>): Summary a summarised_result

suppress(<summarised_result>): Function to suppress counts in result objects

tidy(<summarised_result>) experimental: Turn a <summarised_result> object into a tidy tibble

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

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

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

strataColumns(): Identify variables in strata_name column

additionalColumns(): Identify variables in additional_name column

groupColumns(): Identify variables in group_name column

settingsColumns(): Identify settings columns of a <summarised_result>

tidyColumns(): Identify tidy columns of a <summarised_result>

pivotEstimates(): Set estimates as columns

addSettings(): Add settings columns to a <summarised_result> object

codelist utility functions

Utility functions for codelist objects

exportCodelist(): Export a codelist object.

exportConceptSetExpression(): Export a concept set expression.

importCodelist(): Import a codelist.

importConceptSetExpression(): Import a concept set expression.

print(<codelist>): Print a codelist

print(<codelist_with_details>): Print a codelist with details

print(<conceptSetExpression>): Print a concept set expression

Work with indexes

Methods and functions to work with indexes in database backends.

existingIndexes() experimental: Existing indexes in a cdm object

expectedIndexes() experimental: Expected indexes in a cdm object

statusIndexes() experimental: Status of the indexes

createIndexes() experimental: Create the missing indexes

createTableIndex() experimental: Create a table index

Argument validation

To validate input arguments of the functions

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.

General assertions

To assert that an object fulfills certain criteria

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.

Utility functions

insertFromSource() deprecated: 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.

sourceType(): Get the source type of an object.

tmpPrefix(): Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.

uniqueId(): Get a unique Identifier with a certain number of characters and a prefix.

uniqueTableName(): Create a unique table name

isTableEmpty(): Check if a table is empty or not

toSnakeCase(): Convert a character vector to snake case

combineStrata(): Provide all combinations of strata levels.

createLogFile(): Create a log file

logMessage(): Log a message to a logFile

summariseLogFile(): Summarise and extract the information of a log file into a summarised_result object.

Deprecated

Deprecated function that will be eliminated in future releases of the package

checkCohortRequirements() deprecated: Check whether a cohort table satisfies requirements

dropTable() deprecated: Drop a table from a cdm object.