Changelog

Source: NEWS.md

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.