genderConceptIds argument to
Dropping dependency on
Handling edge case in
computeMdrr() when all observed time is exposed. (Returning
Inf instead of throwing an error.)
allowRegularization in calendar time settings.
When person has multiple nesting cohort entries, prevent double-counting of cases in attrition table if nesting cohort entries have no outcome.
studyEndDatearguments have been changed back to strings instead of dates to facilitate easier conversion to and from JSON.
oracleTempSchema argument from
Adding checking of user input to all functions.
studyEndDate arguments of the
getDbSccsData() function have been changed from character to Date type.
Dropping support of split points. This can be achieved by creating multiple era covariates with different times at risk.
computeMdrr() now works with either an
SccsIntervalData or an
Major overhaul of the multiple-analyses framework:
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).
createExposureOutcome() function has been replaced with the
createExposuresOutcome() function, which accepts multiple objects of type
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
The reference table (the output of
runSccsAnalyses()) can now always be retrieved using the
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
Settings related to multi-threading are combined in to a single settings object that be created using the new
design argument of the
createSccsAnalysis() function has been removed, and the
createScriIntervalDataArgs arguments have been replaced with a single
createIntervalDataArgs argument that accepts arguments for both the
createSccsIntervalData() and createScriIntervalData()` functions.
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.
deleteCovariatesSmallCount argument to 0 in the
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.
computeTimeStability() to 1.25 (instead of 1.1) to avoid false positives.
Fixing “RIGHT and FULL OUTER JOINs are not currently supported” error on SQLite when using
computeTimeStability() per-month p-value (was showing the minimum p-value for all months).
Fixing uncaught errors when fitting models caused by Cyclops’s new return flags.
Fix error about Andromeda object already being closed when generating SCCS era data.
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.
maxRatio argument to
Fixing missing months in
plotEventToCalendarTime() when there are no observation period starts and ends in those months.
Now limiting the number of unexposed cases when including only a calendar time spline (as set by
Fix error when calling
computeMdrr() on an
sccsIntervalData object that does not contain the exposure of interest.
Fixed typo in
Adding optional calendar time covariate.
analysesToExclude argument to
runSccsAnalyses(), allowing the users to specify exposure-outcome-analysis combinations to exclude from execution.
Fixing seed for regularization cross-validation to improve reproducibility.
Adding likelihood profile to SCCS model objects if
profileLikelihood argument is set to
TRUE when calling
oracleTempSchema argument in favor of
tempEmulationSchema in accordance with new
title argument to all plotting functions.
highlightExposedEvents argument to
Switching power calculation default method to signed root likelihood ratio as recommended by Musonda et al. (2005).
Prevent error when excluding variable not in data from regularization.
Removing unexposed subjects when computing power to avoid overestimating statistical power.
Adding the self-controlled risk interval design.
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).
Outputting log likelihood ratio as part of estimates.
Computing meta-data on covariates.
Fixed syntax error in SQL when using a nesting cohort.
Fixing error when sampled cohort is empty.
Attrition table now also includes lines where remaining count is zero.
Fixing custom covariates download.
Fixing error on Oracle due to long temp table name.
Fixing computation of confidence intervals (CIs) when not all estimates for which CIs are computed have data.
Switching from ff to Andromeda for storing large data objects.
Making creation of the study population a separate step, with the new
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’.
Adding tracking of attrition.
Automatically removing age spline if selected censoring model already adjusts for age.
Generating sequential case IDs instead of observation period IDs to avoid collisions due to loss of precision when converting BIGINT to R’s numeric.
Added more heuristics to detect ill-behaving censoring functions when adjusting for event-dependent censoring.
Fixed errors introduced by R 4.0.0.
Gracefully handling when fitting the outcome model hits the max number of iterations.