Package index • CohortGenerator

Cohort Generation

Functions that support generating cohorts.

runCohortGeneration(): Run a cohort generation and export results

generateCohortSet(): Generate a set of cohorts

Cohort Tables

Functions that support creating the necessary cohort tables.

createCohortTables(): Create cohort tables

getCohortTableNames(): Used to get a list of cohort table names to use when creating the cohort tables

Cohort Defintion Set

Functions that support working with a cohort definition set

saveCohortDefinitionSet(): Save the cohort definition set to the file system

getCohortDefinitionSet(): Get a cohort definition set

createEmptyCohortDefinitionSet(): Create an empty cohort definition set

checkAndFixCohortDefinitionSetDataTypes(): Check if a cohort definition set is using the proper data types

isCohortDefinitionSet(): Is the data.frame a cohort definition set?

Cohort Counts

Function for obtaining the counts of subjects and events for one or more cohorts

getCohortCounts(): Count the cohort(s)

Cohort Subset Functions

Functions for creating cohort subset definitions and subset operators.

addCohortSubsetDefinition(): Add cohort subset definition to a cohort definition set

createCohortSubset(): A definition of subset functions to be applied to a set of cohorts

createCohortSubsetDefinition(): Create Subset Definition

createDemographicSubset(): Create createDemographicSubset Subset

createLimitSubset(): Create Limit Subset

createSubsetCohortWindow(): Create a relative time window for cohort subset operations

getSubsetDefinitions(): Get cohort subset definitions from a cohort definition set

saveCohortSubsetDefinition(): Save cohort subset definitions to json

Cohort Subset Classes

R6 classes for cohort subset definitions and subset operators.

CohortSubsetDefinition: Cohort Subset Definition

CohortSubsetOperator: Cohort Subset Operator

DemographicSubsetOperator: Demographic Subset Operator

LimitSubsetOperator: Limit Subset Operator

SubsetCohortWindow: Time Window For Cohort Subset Operator

SubsetOperator: Abstract base class for subsets.

Cohort Statistics

Functions for inserting inclusion rule names from a cohort definition, exporting the cohort statistics to the file system and a helper function for dropping those tables when they are no longer needed. These functions assume you are using Circe for inclusion rules and cohort statistics.

getCohortStats(): Get Cohort Inclusion Stats Table Data

getCohortInclusionRules(): Get Cohort Inclusion Rules from a cohort definition set

insertInclusionRuleNames(): Used to insert the inclusion rule names from a cohort definition set when generating cohorts that include cohort statistics

exportCohortStatsTables(): Export the cohort statistics tables to the file system

dropCohortStatsTables(): Drop cohort statistics tables

Negative Control Outcomes

Functions for creating negative control outcome cohorts for use in population-level estimation.

createEmptyNegativeControlOutcomeCohortSet(): Create an empty negative control outcome cohort set

generateNegativeControlOutcomeCohorts(): Generate a set of negative control outcome cohorts

Result Model Management

Functions for managing the results of running Cohort Generator via runCohortGeneration

createResultsDataModel(): Create the results data model tables on a database server.

getDataMigrator(): Get database migrations instance

getResultsDataModelSpecifications(): Get specifications for CohortGenerator results data model

migrateDataModel(): Migrate Data model

uploadResults(): Upload results to the database server.

CSV File Helpers

Functions for reading and writing CSV files to ensure adherance to the HADES standard when interfacing between R and SQL/File System: https://ohdsi.github.io/Hades/codeStyle.html#Interfacing_between_R_and_SQL

readCsv(): Used to read a .csv file

writeCsv(): Used to write a .csv file

isCamelCase(): Used to check if a string is in lower camel case

isSnakeCase(): Used to check if a string is in snake case

isFormattedForDatabaseUpload(): Is the data.frame formatted for uploading to a database?

Record Keeping

Functions that support record keeping of tasks performed. CohortGenerator uses these functions when running in incremental mode to only generate cohorts when their definition has changed from a previous run.

getRequiredTasks(): Get a list of tasks required when running in incremental mode

recordTasksDone(): Record a task as complete

isTaskRequired(): Is a task required when running in incremental mode

saveIncremental(): Used in incremental mode to save values to a file

computeChecksum(): Computes the checksum for a value

Cohort Sampling

Functions that support sampling a cohort. Please note this is only for software development purposes and NOT for running studies.

sampleCohortDefinitionSet(): Sample Cohort Definition Set

Sample Data

Sample data used in vignettes to showcase how to perform cohort subsets.

omopCdmDrugExposure: OMOP CDM Drug Exposure Sample Data

omopCdmPerson: OMOP CDM Person Sample Data