Cohort Generation for the OMOP Common Data Model


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Documentation for package ‘CohortGenerator’ version 0.11.2

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addCohortSubsetDefinition Add cohort subset definition to a cohort definition set
checkAndFixCohortDefinitionSetDataTypes Check if a cohort definition set is using the proper data types
CohortSubsetDefinition Cohort Subset Definition
CohortSubsetOperator Cohort Subset Operator
computeChecksum Computes the checksum for a value
createCohortSubset A definition of subset functions to be applied to a set of cohorts
createCohortSubsetDefinition Create Subset Definition
createCohortTables Create cohort tables
createDemographicSubset Create createDemographicSubset Subset
createEmptyCohortDefinitionSet Create an empty cohort definition set
createEmptyNegativeControlOutcomeCohortSet Create an empty negative control outcome cohort set
createLimitSubset Create Limit Subset
createResultsDataModel Create the results data model tables on a database server.
createSubsetCohortWindow A definition of subset functions to be applied to a set of cohorts
DemographicSubsetOperator Demographic Subset Operator
dropCohortStatsTables Drop cohort statistics tables
exportCohortStatsTables Export the cohort statistics tables to the file system
generateCohortSet Generate a set of cohorts
generateNegativeControlOutcomeCohorts Generate a set of negative control outcome cohorts
getCohortCounts Count the cohort(s)
getCohortDefinitionSet Get a cohort definition set
getCohortInclusionRules Get Cohort Inclusion Rules from a cohort definition set
getCohortStats Get Cohort Inclusion Stats Table Data
getCohortTableNames Used to get a list of cohort table names to use when creating the cohort tables
getDataMigrator Get database migrations instance
getRequiredTasks Get a list of tasks required when running in incremental mode
getResultsDataModelSpecifications Get specifications for CohortGenerator results data model
getSubsetDefinitions Get cohort subset definitions 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
isCamelCase Used to check if a string is in lower camel case
isCohortDefinitionSet Is the data.frame a cohort definition set?
isFormattedForDatabaseUpload Is the data.frame formatted for uploading to a database?
isSnakeCase Used to check if a string is in snake case
isTaskRequired Is a task required when running in incremental mode
LimitSubsetOperator Limit Subset Operator
migrateDataModel Migrate Data model
readCsv Used to read a .csv file
recordTasksDone Record a task as complete
runCohortGeneration Run a cohort generation and export results
sampleCohortDefinitionSet Sample Cohort Definition Set
saveCohortDefinitionSet Save the cohort definition set to the file system
saveCohortSubsetDefinition Save cohort subset definitions to json
saveIncremental Used in incremental mode to save values to a file
SubsetCohortWindow Time Window For Cohort Subset Operator
SubsetOperator Abstract base class for subsets.
uploadResults Upload results to the database server.
writeCsv Used to write a .csv file