Changelog

Source: NEWS.md

SelfControlledCaseSeries 5.3.0

Changes

  1. Added controlType argument to runSccsAnalyses(), explicitly setting the type of (negative) controls: outcome controls or exposure controls. Setting to “outcome” (the default) will now group by exposure (and nesting cohort if defined).

SelfControlledCaseSeries 5.2.3

Changes

  1. More informative error messages when analysis specifications are inconsistent.

  2. Throwing error when defining an analysis that does not specify at least one era covariate that is the exposure of interest.

  3. The includeEraIds argument of createEraCovariateSettings() no longer has a default, forcing users to explicitly set this to avoid erroneously specifying all covariates.

Bugfixes

  1. Fixed ‘ORDER BY is ignored in subqueries without LIMIT’ warning when calling createSccsIntervalData().

  2. Fixed ‘std::bad_alloc’ error when any observation period start date is before 1970.

  3. Fixed NA covariate values when age, season, or calendar time splines are removed because there are fewer cases than knots.

SelfControlledCaseSeries 5.2.2

Bugfixes

  1. Fix export when there are multiple exposure-outcomes per SCCS data file.

SelfControlledCaseSeries 5.2.1

Bugfixes

  1. Fix exposures_outcome_set_id field in ‘sccs_exposure’ and ‘sccs_exposures_outcome_set’ tables.

SelfControlledCaseSeries 5.2.0

Changes

  1. Switching exposures_outcome_set_id from a sequential number to a hash to avoid issues when dividing a set of analyses over various machines, and combining the results later.

Bugfixes

  1. Fixed error in SQL about “#case_in_period”.

  2. Fixed case count in createStudyPopulation() when restricting time in prior getDbSccsData() call, e.g. by defining a study period and/or nesting cohort.

  3. Preventing duplicate calendar time and age knots, causing unique key violation errors when uploading.

SelfControlledCaseSeries 5.1.1

Bugfixes

  1. Fixed ‘oneSidedP not found’ error when unable to fit a model.

SelfControlledCaseSeries 5.1.0

Changes

  1. Allowing nesting cohort ID to be specified as part of the exposure-outcome pair.

  2. Deprecating the useCustomCovariates and useNestingCohort arguments of the getDbSccsData() function.

  3. Optimized runSccsAnalyses() to allow running bigger sets of analyses.

  4. Adding sccs_time_period table to export, capturing the calendar time period included in the analysis.

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

  6. exportToCsv() can now use multithreading for speed.

  7. Adding unblindForEvidenceSynthesis field to sccs_diagnostics_summary_table.

  8. Unblinding logic now same as for CohortMethod: also unblind if a diagnostic is not evaluated (instead of only unblinding when passing).

Bugfixes

  1. Handling edge case in computeTimeStability() when there is only 1 month.

  2. Correcting computation of fraction of start month observed for computeTimeStability() (was off by 1/31).

SelfControlledCaseSeries 5.0.0

Changes

  1. Added the restrictTimeToEraId argument to the createStudyPopulation() and createCreateStudyPopulationArgs() functions to allow automatically restricting study time to when the exposure was observed (e.g. when the drug was on the market).

  2. Switching from cubic to quadratic splines for age, season, and calendar time to reduce degrees of freedom.

  3. Deprecating the studyStartDate and studyEndDate arguments of the getDbSccsData() function.

  4. Introducing the studyStartDates and studyEndDates arguments of the getDbSccsData() function. These allow specification of multiple (non-overlapping) study periods. This can for example be useful when one wishes to exclude the time of the COVID-19 pandemic to avoid temporal instability.

  5. The spline for calendar time effects can now be multi-segmented, for multiple study periods. Internal knots are evenly distributed over segments based on the amount of data per segment. Additional boundary knots are automatically added for additional segments.

  6. Changed the stability metric implemented in the computeTimeStability() function in two ways: First, the observed rate of the outcome for each month is now compared against the expected rate. This expected rate considers which persons were observed during that month, and if specified, the adjustment for season and calendar time. Second, instead of considering whether any single month exceeded the threshold, the metric now considers whether the mean ratio across all months exceeds the threshold. Together, this makes the metric more robust, and less likely to declare instability when the majority of data is stable.

  7. Changed the plotEventToCalendarTime() to show the observed-to-expected ratio, both with and without adjustments for season and calendar time (if specified in the model).

Bugfix

  1. Using BIGINT when summing patient days to avoid errors when populations are large.

SelfControlledCaseSeries 4.2.0

Changes

  1. Adding the genderConceptIds argument to createStudyPopulation().

  2. Dropping dependency on survival.

Bugfix

  1. Handling edge case in computeMdrr() when all observed time is exposed. (Returning Inf instead of throwing an error.)

  2. Not ignoring allowRegularization in calendar time settings.

  3. When person has multiple nesting cohort entries, prevent double-counting of cases in attrition table if nesting cohort entries have no outcome.

SelfControlledCaseSeries 4.1.0

Changes

  1. The studyStartDate and studyEndDate arguments have been changed back to strings instead of dates to facilitate easier conversion to and from JSON.

Bug fixes

  1. Minor fix related to upcoming DatabaseConnector V6.0.0.

SelfControlledCaseSeries 4.0.0

Changes

  1. Removing deprecated oracleTempSchema argument from getDbSccsData() and runSccsAnalyses() functions.

  2. Adding checking of user input to all functions.

  3. The studyStartDate and studyEndDate arguments of the getDbSccsData() function have been changed from character to Date type.

  4. Dropping support of split points. This can be achieved by creating multiple era covariates with different times at risk.

  5. The computeMdrr() now works with either an SccsIntervalData or an SccsModel object.

  6. Major overhaul of the multiple-analyses framework:

    • Added the createExposure() function for creating objects of type `exposure. This argument allows specifying the true effect size of the exposure, if known (e.g. for negative controls).

    • The createExposureOutcome() function has been replaced with the createExposuresOutcome() function, which accepts multiple objects of type exposure.

    • The createEraCovariateSettings() function has a new argument exposureOfInterest which determines if its estimate will be reported in the result summary.

    • The results summary table has been pivoted so it now only has one estimate per row. The results summary table is now precomputed as part of runSccsAnalyses(), automatically includes empirically calibrated estimates (if controls have been provided) and can be retrieved using the getResultsSummary() function.

    • The reference table (the output of runSccsAnalyses()) can now always be retrieved using the getFileReference() function.

    • Dropping exposureType and outcomeType options from the createSccsAnalysis () function, since the notion of analysis-specific exposure and outcome selection strategies can also be implemented using the analysesToExclude argument of runSccsAnalyses().

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

    • The design argument of the createSccsAnalysis() function has been removed, and the createSccsIntervalDataArgs and createScriIntervalDataArgs arguments have been replaced with a single createIntervalDataArgs argument that accepts arguments for both the createSccsIntervalData() and createScriIntervalData()` functions.

  7. Added the exportToCsv() function, to export the results of a multi-analysis study to CSV files for sharing between sites. The output results model is now documented in a new vignette.

SelfControlledCaseSeries 3.4.0

Changes

  1. Setting the deleteCovariatesSmallCount argument to 0 in the getDbSccsData() and createGetDbSccsDataArgs() functions. This was originally set to 100 for SCCS analyses with many covariates, but makes no sense when considering only one or a few exposures.

  2. Adding the computePreExposureGainP() function.

  3. Setting default maxRatio in computeTimeStability() to 1.25 (instead of 1.1) to avoid false positives.

Bug fixes

  1. Fixing “RIGHT and FULL OUTER JOINs are not currently supported” error on SQLite when using drug_era or condition_era table.

  2. Fixing computeTimeStability() per-month p-value (was showing the minimum p-value for all months).

  3. Fixing uncaught errors when fitting models caused by Cyclops’s new return flags.

  4. Fix error about Andromeda object already being closed when generating SCCS era data.

SelfControlledCaseSeries 3.3.0

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. Added maxRatio argument to computeTimeStability().

Bug fixes

  1. Fixing missing months in plotEventToCalendarTime() when there are no observation period starts and ends in those months.

  2. Now limiting the number of unexposed cases when including only a calendar time spline (as set by minCasesForTimeCovariates).

  3. Fix error when calling computeMdrr() on an sccsIntervalData object that does not contain the exposure of interest.

  4. Fixed typo in computeMdrr(), renaming propPopExposued to propPopulationExposed.

SelfControlledCaseSeries 3.2.1

BugFixes

  1. Remove dependency on develop branch of SqlRender.

SelfControlledCaseSeries 3.2.0

Changes

  1. Adding optional calendar time covariate.

  2. Added the analysesToExclude argument to runSccsAnalyses(), allowing the users to specify exposure-outcome-analysis combinations to exclude from execution.

  3. Fixing seed for regularization cross-validation to improve reproducibility.

  4. Added the computeTimeStability() function.

SelfControlledCaseSeries 3.1.0

Changes

  1. Adding likelihood profile to SCCS model objects if profileLikelihood argument is set to TRUE when calling createEraCovariateSettings().

  2. Deprecating oracleTempSchema argument in favor of tempEmulationSchema in accordance with new SqlRender convention.

  3. Adding optional title argument to all plotting functions.

  4. Adding highlightExposedEvents argument to plotExposureCentered function.

  5. Switching power calculation default method to signed root likelihood ratio as recommended by Musonda et al. (2005).

BugFixes

  1. Prevent error when excluding variable not in data from regularization.

  2. Removing unexposed subjects when computing power to avoid overestimating statistical power.

SelfControlledCaseSeries 3.0.0

Changes

  1. Adding the self-controlled risk interval design.

  2. Downloading person and observation period IDs as strings to avoid issues with 64-bit integers. (These IDs are not used by SCCS, and are used for reference only).

  3. Outputting log likelihood ratio as part of estimates.

  4. Computing meta-data on covariates.

BugFixes

  1. Fixed syntax error in SQL when using a nesting cohort.

  2. Fixing error when sampled cohort is empty.

  3. Fixing nesting.

  4. Attrition table now also includes lines where remaining count is zero.

  5. Fixing custom covariates download.

  6. Fixing error on Oracle due to long temp table name.

  7. Fixing computation of confidence intervals (CIs) when not all estimates for which CIs are computed have data.

SelfControlledCaseSeries 2.0.0

Changes

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

  2. Making creation of the study population a separate step, with the new createStudyPopulation function.

  3. The data on cohorts, exposure, and outcome eras retrieved from the database is now consistently referred to as ‘eras’. Data transformed to non-overlapping intervals is now referred to as ‘sccsIntervalData’.

  4. Adding tracking of attrition.

  5. Automatically removing age spline if selected censoring model already adjusts for age.

BugFixes

  1. Generating sequential case IDs instead of observation period IDs to avoid collisions due to loss of precision when converting BIGINT to R’s numeric.

  2. Added more heuristics to detect ill-behaving censoring functions when adjusting for event-dependent censoring.

SelfControlledCaseSeries 1.4.2

Bugfixes

  1. Fixed errors introduced by R 4.0.0.

  2. Gracefully handling when fitting the outcome model hits the max number of iterations.

SelfControlledCaseSeries 1.4.1

Bugfixes

  1. Several workaround for issues with the ff package.

  2. Fixed bug causing age to be read incorrectly when creating eras.