New approach #55
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New approach #55
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- see news
removing version from is_installed to fix bug introduced with new R version
fixing test issue caused by converting covariateSettings to a list
see news
fixing checks
fixing example check issues
- removed pdf from package as user can access via website - updated website - renamed vignette called UsingCharacterizationPackage to UsingPackage as name too long for window's R check
updating aggregate characterization to use custom during covariates for case analysis
…inations.sql Fixed case sensitivity
Changed case of CreateTargetOutcomeCombinations.sql
…terization into improving_aggregate
fixing primary key for test to pass
Improving aggregate results model
removing migration and package_version from exports
- added columns to PK for dechal-rechal table - added max rows to export input when doing csv export
- supporting multiple TARs - split aggregate covariate SQL into parts with and without TAR - added time_to_event result table with migrations
fixing time_at_risk tables
- adding checks for unique cohort_definition_ids
- using row_id for FE to not have conflicts - adding hash of settings to be runId for uniqueness and for incremental mode
- runs codes in parallel - has incremental mode - saves direct to csv and then aggregates csvs
- fixing tte and dcrc to export csv files - fixing bug when no results for aggregate covariates - adding tests to get 90% coverage
updating vignette
removing primary key from counts as columns in key can be NULL
- putting Os into T aggregate extraction for efficiency
- created cleaner runCharacterization using do.call - updated cohortTypes for aggregate covariates to be more intuitive - improved incremental - made result folder location more flexible - added parallelization to tte and dechal-rechal - TODO: update for new FE and update aggregate cov job to not run target if desired
- updating min FE version and adding the two columns that new FE requires in covariate_ref - making the non-case aggregate covariate setting work and adding a test for it
- adding log - fixing small bug
removing . in documentation
minor fixes
- added check to ensure single tar per aggregate setting
- adding manual data test - fixed but in target counts found with manual test
- added test to manual data to ensure cohort type Exclude works
- editing setting_id to be float - moving tables/columns in resulttables.sql to be consistent with resultsdatamodelspecifications.csv
- adding random file location to prevent OS test clashes
- updating docs
- adding time delay to ensure setting ids are unique between target and cases
fixing issue with different case tars having same id
- adding edits based on commit to old Characterization by Anthony Sena
- removed code from dechal-rechal to return rows when no dechal as it is much faster - updated tests - fixed missing DatabaseConnection:: in db tests
fixing db tests
- fixing bug where mincellcount wasnt being used by aggregate covs - adding tests for all mincellcount cells - turning off GHA mac spark tests due to odd java error on there (tested manually on my mac)
- updating docs - turning off dbms test except for windows
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