CohortGenerator 0.11.1

CohortGenerator 0.11.0

New Features

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)

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)

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)

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)

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)

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)

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)

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)

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

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

Fixing documentation

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

Initial version