CohortMethod 6.0.1

Changes:

• Adding CohortMethod to CRAN. Required changes:
  • Using message() instead of writeLines() in printing functions.
  • Minor changes to documentation and vignettes.

CohortMethod 6.0.0

This major release introduces many changes. The three most important ones are (1) changing the settings objects, (2) supporting nesting cohorts, and (3) covariate balance significance testing.

Changes related to the settings objects

1. All settings objects have been changed to R6 classes, and are now used both when calling functions individually and when using runCmAnalyses(). The main rationale is that allows 3rd parties to more easily generate valid settings.

2. Dropped the cdmVersion argument in getDbCohortMethodData() and runCmAnalyses(). The version will be identified in the cdm_source table.

3. Dropped the trimByIptw() and trimByPsToEquipoise() functions. Added equipoiseBounds and maxWeight arguments to createTrimByPsArgs() so functionality remains.

4. Dropped the matchOnPsAndCovariates() function and added a stratificationCovariateIds argument to createMatchOnPsArgs() so functionality remains.

5. Dropped the stratifyByPsAndCovariates() function and added a stratificationCovariateIds argument to createStratifyByPsPsArgs() so functionality remains.

6. Renamed createStudyPopArgs argument of createCmAnalysis() to createStudyPopulationArgs for consistency.

7. Dropping the deprecated attritionFractionThreshold argument of createCmDiagnosticThresholds(). The amount of attrition is not a good measure of generalizability. Use the generalizability diagnostic instead, which measures the similarity between the target and analytic cohort characteristcs.

8. Changed the default outcome model type from ‘logistic’ to ‘cox’.

9. Set the defaults of createGetDbCohortMethodDataArgs() to those most often used.

10. Dropped the firstExposureOnly, restrictToCommonPeriod, washoutPeriod, and removeDuplicateSubjects arguments from CreateStudyPopulationArgs. These were duplicated from getDbCohortMethodData(), and we’ll keep them only there from now on.

Changes related to nesting cohorts

11. Added ability to restrict to a nesting cohort (e.g. restricting drug exposures to a specific indication). See the nestingCohortId argument in the createGetDbCohortMethodDataArgs() and createTargetComparatorOutcomes() functions and the nestingCohortDatabaseSchema and nestingCohortTable arguments in the getDbCohortMethodData() function.

12. The results schema now includes the target_comparator table that combines the target_id, comparator_id, and nesting_cohort_id into a single unique target_comparator_id. This new ID is a hash of its components, allowing results from multiple runs to be combined into a single database.

13. In addition to restricting to a nesting cohort the population can now also be restricted by age and gender using the minAge, maxAge, and genderConceptIds arguments of createGetDbCohortMethodDataArgs().

Changes related to the new covariate balance diagnostic

14. Added optional significance testing to covariate balance. This avoids failing the balance diagnostic on smaller databases just because of random chance, and was found to be superior in our methods research. This introduces the following changes to the interface:

    • Added the threshold and alpha arguments to the createComputeCovariateBalanceArgs() function. These do not impact blinding when running runCmAnalyses but do add columns to the balance files, for when running single studies.
    • Added the sdmAlpha argument to the createCmDiagnosticThresholds() function.

    This adds the sdm_family_wise_min_p and shared_sdm_family_wise_min_p fields to the cm_diagnostics_summary table when exporting to CSV. For now, the default is not to use significance testing, but the family-wise min P can help understand if one would have passed when using it.

Other important changes

15. Added a new option for the removeDuplicateSubjects argument: “keep first, truncate to second”. This is similar to “keep first”, but also truncates the first exposure to stop the day before the second starts.

16. Now performing empirical calibration after removing estimates that fail diagnostics. In general this should lead to narrower calibrated confidence intervals.

17. If high correlation is detected when fitting a propensity model, but stopOnError = FALSE, the export will show the highly correlated covariates in the model with extreme coefficients (1e6 * correlation).

18. Added the ability to use bootstrap for computing confidence intervals. See the bootstrapCi and bootstrapReplicates arguments of createFitOutcomeModelArgs().

19. All restrictions on the study populations performed by getDbCohortMethodData() are now step-by-step recorded in the attrition table.

20. Completely updated of all unit tests to increase coverage of functional tests, while also increasing speed.

21. Renamed the showEquipoiseLabel argument of plotPs() to showEquipoiseLabel.

22. Updated the trimByPs() function. This now supports three different trimming functions as described in the literature.

Minor changes

23. Added support for grid-with-gradient likelihood profiles. Use the following arguments in createFitOutcomeModelArgs() to use:

    profileGrid = seq(log(0.1), log(10), length.out = 8),
    profileBounds = NULL

    This adds the gradient field to the cm_likelihood_profile table when exporting to CSV.

24. Removed mention of legacy function grepCovariateNames() from the vignette.

25. Added citation to the HADES paper to the package.

26. Dropped insertExportedResultsInSqlite(), launchResultsViewerUsingSqlite, and launchResultsViewer(). The OhdsiShinyAppBuilder package should be used directly instead.

27. Corrected the minDaysAtRisk argument. Days at risk is now computed as end - start + 1 (end day inclusive).

28. Added a vignette showing the results schema.

29. Changed the data type of the interaction_covariate_id field in the cm_interaction_result table from INT to BIGINT.

30. Fixed trimming by IPTW using trimFraction argument.

CohortMethod 5.5.2

Bugfixes:

1. Reorganized createPs() to be much more efficient for large study populations (millions of patients).

2. Reorganized fitOutcomeModel() to be much more efficient for large study populations (millions of patients).

CohortMethod 5.5.1

Bugfixes:

1. Fixed error thrown by Kaplan Meier curves functions when only one of the cohorts is empty.

CohortMethod 5.5.0

Changes:

1. createPs() now checks if filtering of the covariate data is necessary (either because subject have been removed from the study population or because excludeCovariateIds or includeCovariateIds was specified). If no filtering is required, no extra copy of the covariate data data is created, saving IO time.

2. Added minimumCaseCount argument to createCohortMethodDataSimulationProfile().

3. Preparing for Andromeda 1.0.0: no longer assuming Andromeda tables are sorted.

4. Changing dependency from ShinyAppBuilder to OhdsiShinyAppBuilder.

Bugfixes:

1. Fixed NA covariate prevalences when calling createCohortMethodDataSimulationProfile().

2. Added some optimization to createPs() to prevent running out of memory for large data objects using Andromeda >= 1.0.0.

CohortMethod 5.4.0

Changes:

1. Updating viewer code to work with newer versions of OhdsiShinyModules and ShinyAppBuilder.

2. Dropped uploadExportedResults() function.

3. The cohorts argument of insertExportedResultsInSqlite() has column cohortId renamed to cohortDefinitionId.

4. Added computation of MDRR for logistic models.

CohortMethod 5.3.0

Changes:

1. Switching cohort IDs in results model to BIGINT.

Bugfixes:

1. Fix enforceCellCount() applied to covariate balance when all balance is NA.

2. Stopping fitting PS model early when either target or comparator is empty. Prevents error when target or comparator is empty, sampling is required, and Cyclops happens to fit a model instead of declaring ILL CONDITIONED.

3. Message after matching on PS now shows correct number of subjects remaining after matching.

CohortMethod 5.2.1

Changes:

1. Ask to delete files in output folder when calling runCmAnalyses() with different analyses settings than those used to create the files. Also cleaning the cache.

Bugfixes:

1. Fixed bug in parsing covariate filter settings for balance.

2. Updated vignettes to use latest Capr functions.

CohortMethod 5.2.0

Changes:

1. The computeCovariateBalance() function now also computes standardized difference of mean comparing cohorts before and after PS adjustment, which can inform on generalizability.

2. Added the getGeneralizabilityTable() function.

3. Improved computation of overall standard deviation when computing covariate balance (actually computing the SD instead of taking the mean of the target and comparator). Should produce more accurate balance estimations.

4. Generated population objects now keep track of likely target estimator (e.g. ‘ATT’, or ‘ATE’). This informs selection of base population when calling getGeneralizabilityTable().

5. Deprecated the attritionFractionThreshold argument of the createCmDiagnosticThresholds function, and instead added the generalizabilitySdmThreshold argument.

6. The results schema specifications of the exportToCsv() function has changed:

   • Removed the attrition_fraction and attrition_diagnostic fields from the cm_diagnostics_summary table.
   • Added the target_estimator field to the cm_result add cm_interaction_result tables.
   • Added the generalizability_max_sdm and generalizabiltiy_diagnostic fields to the cm_diagnostics_summary table.
   • Added the mean_before, mean_after, target_std_diff, comparator_std_diff, and target_comparator_std_diff fields to both the cm_covariate_balance and cm_shared_covariate_balance tables.

7. Improve speed of covariate balance computation.

8. Adding one-sided (calibrated) p-values to results summary and results model.

9. Adding unblind_for_evidence_synthesis field to cm_diagnostics_summary table.

10. The cm_diagnostics_summary table now also contains negative controls.

Bugfixes:

1. Fixing runCmAnalyses() when using refitPsForEveryOutcome = TRUE.

2. Handling edge case when exporting preference distribution and the target or comparator only has 1 subject.

CohortMethod 5.1.0

Changes:

1. Now also not unblinding if shared balance diagnostic fails.

Bugfixes:

1. Fixing matching on PS and other covariates.

2. Now passing outcome-specific riskWindowEnd argument in runCmAnalyses() when specified.

3. Fixed error when calling createStudyPopulation() with “keep first” when there is only 1 person in the population.

CohortMethod 5.0.0

Changes:

1. Setting the default Cyclops control object to use resetCoefficients = TRUE to ensure we always get the exact same model, irrespective of the number of threads used.

2. Adding checking of user input to all functions.

3. Removing deprecated excludeDrugsFromCovariates argument from getDbCohortMethodData() function.

4. Removing deprecated oracleTempSchema argument from getDbCohortMethodData() and runCmAnalyses() functions.

5. Removing deprecated addExposureDaysToStart and addExposureDaysToStart arguments from createStudyPopulation() and plotTimeToEvent() functions.

6. The removeDuplicateSubjects argument of getDbCohortMethodData() and createStudyPopulation() is no longer allowed to be a boolean.

7. Adding computeEquipoise() function.

8. Output likelihood profile as data frame instead of named vector for consistency with other HADES packages.

9. Added the covariateFilter argument to the computeCovariateBalance function, to allow balance to be computed only for a subset of covariates.

10. Rounding propensity scores to 10 digits to improve reproducibility across operating systems.

11. Setting covariateCohortDatabaseSchema and covariateCohortTable of cohort-based covariate builders to exposureDatabaseSchema and exposureTable, respectively if covariateCohortTable is NULL.

12. Now computing IPTW in createPs(), and truncating IPTW can be done in truncateIptw(). The computeCovariateBalance() function now computes balance using IPTW if no stratumId column is found in the population argument.

13. Removing PS of exactly 0 and exactly 1 when computing the standard deviation of the logit for the matching caliper to allow matching when some subjects have perfectly predictable treatment assignment.

14. Adding maxRows argument to computePsAuc() function to improve speed for very large study populations.

15. Dropping support for CDM v4.

16. Major overhaul of the multiple-analyses framework:

    • Added the createOutcome() function, to be used with createTargetComparatorOutcomes(). This allow the priorOutcomeLookback, riskWindowStart, startAnchor, riskWindowEnd, and endAnchor arguments to be specified per outcome. These settings (if provided) will override the settings created using the createCreateStudyPopulationArgs() function. In addition, the createOutcome() function has an outcomeOfInterest and trueEffectSize argument (see below).

    • Added the createComputeCovariateBalanceArgs() function, added the computeSharedCovariateBalance, ,computeSharedCovariateBalanceArgs, computeCovariateBalance, and computeCovariateBalanceArgs arguments to the createCmAnalysis() function, and the computeSharedBalanceThreads, computeBalanceThreads arguments to the runCmAnalyses() function to allow computation of covariate balance across a target-comparator-analysis (shared) or for each target-comparator-analysis-outcome in the runCmAnalyses() function.

    • Dropping targetType and comparatorType options from the createCmAnalysis() function, since the notion of analysis-specific target and comparator selection strategies can also be implemented using the analysesToExclude argument of runCmAnalyses().

    • Dropping outcomeIdsOfInterest argument of the runCmAnalyses() function. Instead, the createOutcome() function now has a outcomeOfInterest argument.

    • Settings related to multi-threading are combined in to a single settings object that be created using the new createCmMultiThreadingSettings() function.

    • Dropping prefilterCovariates from runCmAnalyses(). Prefiltering is now always done when specific covariates are used in the outcome model.

    • Removed the summarizeAnalyses() function. Instead, results are automatically summarized in runCmAnalyses(). The summary can be retrieved using the new getResultsSummary() and getInteractionResultsSummary() functions. Empirical calibration, MDRR, and attrition fraction are automatically computed.

    • Changing case in output of getResultsSummary() from ci95lb and ci95ub to ci95Lb and ci95Ub.

    • Added empirical calibration to the getResultsSummary() function. Controls can be identified by the trueEffectSize argument in the createOutcome() function.

    • Dropping arguments like createPs and fitOutcomeModel from the createCmAnalysis() function. Instead, not providing createPsArgs or fitOutcomeModelArgs is assumed to mean skipping propensity score creation or outcome model fitting, respectively.

17. Added the exportToCsv() function for exporting study results to CSV files that do not contain patient-level information and can therefore be shared between sites. The getResultsDataModel() function returns the data model for these CSV files.

18. Added the uploadExportedResults() and insertExportedResultsInSqlite() functions for uploading the results from the CSV files in a database. The launchResultsViewer() and launchResultsViewerUsingSqlite() functions were added for launching a Shiny app to view the results in the (SQLite) database.

Bug fixes:

1. Fixed error when using integer maxWeight when performing IPTW.

CohortMethod 4.2.3

Changes;

1. Removed RISCA from the Suggests list. This package was used for a single unit test, but has a large amount of difficult-to-install dependencies.

Bug fixes:

1. Fixed error when failing model fitting caused by new Cyclops version.

CohortMethod 4.2.2

Changes:

1. Added the analysesToExclude argument to runCmAnalyses, allowing the users to specify target-comparator-outcome-analysis combinations to exclude from execution.

2. Output of computeCovariateBalance() now also contains domainId and isBinary columns.

3. Added plotCovariatePrevalence() function.

Bug fixes:

1. Fixed erroneous sample size reported for comparator cohorts when computing covariate balance. (the actual sample size was fine)

2. Fixed error when all analyses have fitOutcomeModel = FALSE.

3. Fixed attrition counts when using allowReverseMatch = TRUE

CohortMethod 4.2.1

Changes:

1. Adding highlightExposedEvents and includePostIndexTime arguments to plotTimeToEvent().

2. Adding maxCohortSize argument to the computeCovariateBalance() function. The target and comparator cohorts will be downsampled if they are larger, speeding up computation.

Bug fixes:

1. Fixed error thrown by plotTimeToEvent() when there are time periods in plot when nobody is observed.

CohortMethod 4.2.0

Changes:

1. Adding the trimByIptw() function.

2. Adding the estimator argument to the fitOutcomeModel() function to select ‘ate’ (average treatment effect) or ‘att’ (average treatment effect in the treated) when performing IPTW.

3. Added the maxWeight argument to the fitOutcomeModel() function. Weights greater than this value will be set to this value.

4. Adding option to use adaptive likelihood profiling, and making this the default.

5. Adding maxDaysAtRisk argument to the createStudyPopulation() and createCreateStudyPopulationArgs() functions.

Bug fixes:

1. Fixing IPTW.

2. Fixing error when stratifying and base population is empty (but overall population is not).

CohortMethod 4.1.0

Changes:

1. Dropped insertDbPopulation() function. This didn’t seem to be used by anyone, and would have required carrying the person ID throughout the pipeline.

2. Introducing new unique person identified called personSeqId, generated during data extraction. Person ID is now downloaded as string to avoid issues with 64-bit integers. Person ID is not used by CohortMethod, and is provided for reference only.

3. Adding log likelihood ratio to outcome model object.

4. Deprecating oracleTempSchema argument in favor of tempEmulationSchema in line with new SqlRender interface.

Bug fixes:

1. Still was not always including the likelihood profile in the outcome model objects.

2. Fixing issues when IDs are integer64.

CohortMethod 4.0.1

Changes:

1. Always including the likelihood profile in the outcome model objects.

Bug fixes:

1. Fixing “argument ‘excludeDrugsFromCovariates’ is missing” error when calling createGetDbCohortMethodDataArgs() without deprecated argument excludeDrugsFromCovariates.

2. More testing and handling of empty exposure cohorts.

3. Fixing exclusion of covariate IDs when fitting propensity models.

4. Correct covariate balance computation when covariate values are integers.

CohortMethod 4.0.0

Changes:

1. Switching from ff to Andromeda for storing large data objects.

Bugfixes:

1. Fixed bug in IPTW.

CohortMethod 3.1.1

Changes:

1. Updating documentation: adding literature reference for IPTW, and using new SqlRender interface in vignettes.

2. Changing default equipoise bounds from 0.25-0.75 to 0.3-0.7 to be consistent with Alec Walker’s original paper.

Bugfixes:

1. Fixing some issues when sampling before fitting propensity models.

CohortMethod 3.1.0

Changes:

1. Added plotTimeToEvent function

2. Deprecating addExposureDaysToStart and addExposureDaysToEnd arguments, adding new arguments called startAnchor and endAnchor. The hope is this is less confusing.

3. Fixing random seeds for reproducibility.

4. Changing default equipoise bounds from 0.25-0.75 to 0.3-0.7 to be consistent with Alec Walker’s original paper.

Bugfixes:

1. No longer overriding ffmaxbytes and ffbatchbytes in .onLoad. Instead relying on FeatureExtraction to do that. Part of fixing chunk.default error caused by ff package on R v3.6.0 on machines with lots of memory.

2. Correct calculation in original population count when using study end date.

CohortMethod 3.0.2

Changes:

1. (Much) faster variable ratio matching