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(): Create Cohort Subset Operator
createCohortSubsetOperator(): A definition of subset functions to be applied to a set of cohorts
createCohortSubsetDefinition(): Create Subset Definition
createDemographicSubset(): Create Demographic Subset Operator
createDemographicSubsetOperator(): Create createDemographicSubset Subset operator
createLimitSubset(): Create Limit Subset Operator
createLimitSubsetOperator(): Create Limit Subset Operator
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 Recipies

Standard functions for creating subsets that wrap more complex operations

addExcludeOnIndexSubsetDefinition(): Add exclude on index subset definition
addIndicationSubsetDefinition(): Add Indication Subset Definition
addRestrictionSubsetDefinition(): Add Restriction Subset Definition
getExcludeOnIndexSubsetDefinitionIds(): Get Exclude On Index Subset Definition Ids
getIndicationSubsetDefinitionIds(): Get Indication Subset Definition Ids
getRestrictionSubsetDefinitionIds(): Get Restriction Subset Definition Ids

Cohort Template Functions

Utilities for creating template cohort definitions from raw sql

CohortTemplateDefinition: Class for automating the creation of bulk cohorts
addCohortTemplateDefintion(): Add Cohort template definition to cohort set
addSqlCohortDefinition(): Add an sql cohort definition
addUnionCohortDefinition(): Add union cohort definition to cohort definition set
createAtcCohortTemplateDefinition(): Create ATC Cohort Template Definition
createCohortTemplateDefintion(): Create Cohort Template Definition
createRxNormCohortTemplateDefinition(): Create Rx Norm Cohort Template Definition
createSnomedCohortTemplateDefinition(): Create SNOMED Cohort Template Definition
createUnionCohortTemplate(): Create cohort template to union multiple cohorts
getCohortValidationCounts(): Validate cohort
getTemplateDefinitions(): Extract template definitions from a cohort definition set

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.

getLastGeneratedCohortChecksums(): Get last generated cohort checksums
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