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Changelog

Source: NEWS.md

CohortGenerator 0.12.2

  • Updates unit tests to use lowercase field names (#237)

CohortGenerator 0.12.1

CRAN release: 2025-09-05

Bug Fixes - Fix logical issue with null minimum cohort duration

CohortGenerator 0.12.0

CRAN release: 2025-07-31

New Features

  • Backwards compatable extension to CohortSubsetOperators and cohortSubsetWindows to allow windowing to be logic of any length
  • Include observation table when creating negative control cohorts (#198)
  • Improvements to cohort subset documentation (#199)
  • Add negate parameter to createSubsetCohortWindow function (#217)

Bug Fixes - Remove RJSONIO from dependency list (#202) - Upgrade GitHub Actions to use Ubuntu 22.04 (#204) - Add missing database_id as primary key of cg_cohort_censor_stats (#215) - saveIncremental prevents saving empty files (#212) - Subset identifier expressions are not deserialized (#225)

CohortGenerator 0.11.2

CRAN release: 2024-09-30

  • Ensure temp tables are dropped before creating them (#188)

CohortGenerator 0.11.1

CRAN release: 2024-09-15

  • CohortGenerator added to CRAN (#77)

CohortGenerator 0.11.0

New Features

  • Add support for minimum cell count (#176)

Bug Fixes

  • Multiple calls to export stats causing duplicates in cohort inclusion file (#179)
  • Updates to subset documentation (#180, #181)
  • Negative control outcome generation bug (#177)

CohortGenerator 0.10.0

New Features

  • Add runCohortGeneration function (Issue #165)
  • Adopt ResultModelManager for handling results data models & uploading. Extend results data model to include information on cohort subsets(#154, #162)
  • Remove REMOTES entries for CirceR and Eunomia which are now in CRAN (#145)
  • Unit tests now running on all OHDSI DB Platforms (#151)

Bug Fixes

  • Negation of cohort subset operator must join on subject_id AND start_date (#167)
  • Allow integer as cohort ID (#146)
  • Use native messaging functions for output vs. ParallelLogger (#97)
  • Prevent upload of inclusion rule information (#78)
  • Expose colTypes when working with .csv files (#59)
  • Remove bit64 from package (mostly) (#152)
  • Updated documentation for cohort subset negate feature (#111)

CohortGenerator 0.9.0

  • Random sample functionality (for development only) (Issue #129)
  • Incremental mode for negative control cohort generation (Issue #137)
  • Fixes getCohortCounts() if cohortIds is not specified, but cohortDefinitionSet is. (Issue #136)
  • Add cohort ID to generation output messages (Issue #132)
  • Add databaseId to output of getStatsTable() (Issue #116)
  • Prevent duplicate cohort IDs in cohortDefinitionSet (Issue #130)
  • Fix cohort stats query for Oracle (Issue #143)
  • Ensure databaseId applied to all returned cohort counts (Issue #144)
  • Preserve backwards compatibility if cohort sample table is not in the list of cohort table names (Issue #147)

CohortGenerator 0.8.1

  • Include cohorts with 0 people in cohort counts (Issue #91).
  • Use numeric for cohort ID (Issue #98)
  • Allow big ints for target pairs (#103)
  • Pass tempEmulationSchema when creating negative control cohorts (#104)
  • Target CDM v5.4 for unit tests (#119)
  • Fix for subset references (#115)
  • Allow for subset cohort name templating (#118)
  • Allow all entries with limit operator and do not require > 0 days follow up (#112)

CohortGenerator 0.8.0

  • New feature: cohort subsetting (Issue #67).
  • Removes the evaluation of ROhdsiWebApi code in vignettes (Issue #70)
  • Basic tests for different database platforms (#71)

CohortGenerator 0.7.0

  • Fixes data type issue for Google Big Query (Issue #51).
  • Removes the databaseId field from the cohort inclusion table (Issue #52)
  • Adds the ability to generate negative control outcome cohorts for use in population-level estimation. (Issue #9)

CohortGenerator 0.6.0

  • Add more flexibility when reading/writing CSV files including appending (Issue #44), flags for disabling warnings (Issue #38) and removing unhelpful warnings (Issue #43).
  • Added better error handling to saveCohortDefinitionSet (Issue #25)
  • Add better handling of column name casing in CSV files that hold cohort settings. (Issue #37)
  • Added functions to check if a data.frame conforms to a cohortDefinitionSet (Issue #21)

CohortGenerator 0.5.0

  • Allow for specification of the database_id in export methods. (Issue #18)
  • getCohortStats function allows for exporting cohort statistics into data frames (Pull Request #24)
  • Add utility methods for reading/writing CSV files. (Issue #16)

CohortGenerator 0.4.0

  • Update dependency versions in DESCRIPTION to resolve issues when using older versions of readr/stringi. (Issue #13)
  • Breaking change: change the defaults for saving/getting a cohortDefinitionSet to/from the file system. (Issue #16)
  • getCohortCounts now supports an optional parameter cohortDefinitionSet which will join the cohort counts with the cohort definition set when desired (Issue #14)

CohortGenerator 0.3.0

  • Added getCohortDefintionSet function for retrieving a cohort definition set from either a package or the file system
  • Re-factored saveCohortDefinitionSet to remove the settingsFolder. The settingsFileName should include the path to the file.
  • Bug fixes

CohortGenerator 0.2.0

  • Renamed createCohortTable to createCohortTables to include all cohort statistics tables
  • Renamed createEmptyCohortSet to createEmptyCohortDefinitionSet to make this consistent with ROhdsiWebApi and CohortDiagnostics
  • Added dropCohortStatsTables function for removing cohort statistics tables
  • Added exportCohortStatsTables function for exporting cohort statistics to CSV files
  • Added getCohortTableNames function to define the list of cohort table names to create
  • Added insertInclusionRuleNames for inserting the inclusion rule names into the cohort stats table
  • Added saveCohortDefinitionSet to save the cohort definition set to the file system for use by study packages
  • Added a vignette and updated documentation
  • Remove CirceR dependency and related functions

CohortGenerator 0.1.1

Fixing documentation

CohortGenerator 0.1.0

Updating function calls to use “generate” instead of “instantiate”

CohortGenerator 0.0.1

Initial version