NEWS.md
Changes:
Bugfixes:
Fix enforceCellCount()
applied to covariate balance when all balance is NA.
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.
Message after matching on PS now shows correct number of subjects remaining after matching.
Changes:
runCmAnalyses()
with different analyses settings than those used to create the files. Also cleaning the cache.Bugfixes:
Fixed bug in parsing covariate filter settings for balance.
Updated vignettes to use latest Capr
functions.
Changes:
The computeCovariateBalance()
function now also computes standardized difference of mean comparing cohorts before and after PS adjustment, which can inform on generalizability.
Added the getGeneralizabilityTable()
function.
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.
Generated population objects now keep track of likely target estimator (e.g. ‘ATT’, or ‘ATE’). This informs selection of base population when calling getGeneralizabilityTable()
.
Deprecated the attritionFractionThreshold
argument of the createCmDiagnosticThresholds
function, and instead added the generalizabilitySdmThreshold
argument.
The results schema specifications of the exportToCsv()
function has changed:
attrition_fraction
and attrition_diagnostic
fields from the cm_diagnostics_summary
table.target_estimator
field to the cm_result
add cm_interaction_result
tables.generalizability_max_sdm
and generalizabiltiy_diagnostic
fields to the cm_diagnostics_summary
table.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.Improve speed of covariate balance computation.
Adding one-sided (calibrated) p-values to results summary and results model.
Adding unblind_for_evidence_synthesis
field to cm_diagnostics_summary
table.
The cm_diagnostics_summary
table now also contains negative controls.
Bugfixes:
Fixing runCmAnalyses()
when using refitPsForEveryOutcome = TRUE
.
Handling edge case when exporting preference distribution and the target or comparator only has 1 subject.
Changes:
Bugfixes:
Fixing matching on PS and other covariates.
Now passing outcome-specific riskWindowEnd
argument in runCmAnalyses()
when specified.
Fixed error when calling createStudyPopulation()
with “keep first” when there is only 1 person in the population.
Changes:
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.
Adding checking of user input to all functions.
Removing deprecated excludeDrugsFromCovariates
argument from getDbCohortMethodData()
function.
Removing deprecated oracleTempSchema
argument from getDbCohortMethodData()
and runCmAnalyses()
functions.
Removing deprecated addExposureDaysToStart
and addExposureDaysToStart
arguments from createStudyPopulation()
and plotTimeToEvent()
functions.
The removeDuplicateSubjects
argument of getDbCohortMethodData()
and createStudyPopulation()
is no longer allowed to be a boolean.
Adding computeEquipoise()
function.
Output likelihood profile as data frame instead of named vector for consistency with other HADES packages.
Added the covariateFilter
argument to the computeCovariateBalance
function, to allow balance to be computed only for a subset of covariates.
Rounding propensity scores to 10 digits to improve reproducibility across operating systems.
Setting covariateCohortDatabaseSchema
and covariateCohortTable
of cohort-based covariate builders to exposureDatabaseSchema
and exposureTable
, respectively if covariateCohortTable
is NULL
.
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.
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.
Adding maxRows
argument to computePsAuc()
function to improve speed for very large study populations.
Dropping support for CDM v4.
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.
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.
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:
maxWeight
when performng IPTW.Changes;
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:
Cyclops
version.Changes:
Added the analysesToExclude
argument to runCmAnalyses
, allowing the users to specify target-comparator-outcome-analysis combinations to exclude from execution.
Output of computeCovariateBalance()
now also contains domainId
and isBinary
columns.
Added plotCovariatePrevalence()
function.
Bug fixes:
Fixed erroneous sample size reported for comparator cohorts when computing covariate balance. (the actual sample size was fine)
Fixed error when all analyses have fitOutcomeModel = FALSE
.
Fixed attrition counts when using allowReverseMatch = TRUE
Changes:
Adding highlightExposedEvents
and includePostIndexTime
arguments to plotTimeToEvent()
.
Adding maxCohortSize
argument to the computeCovariateBalance()
function. The target and comparator cohorts will be downsampled if they are larger, speeding up computation.
Bug fixes:
plotTimeToEvent()
when there are time periods in plot when nobody is observed.Changes:
Adding the trimByIptw()
function.
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.
Added the maxWeight
argument to the fitOutcomeModel()
function. Weights greater than this value will be set to this value.
Adding option to use adaptive likelihood profiling, and making this the default.
Adding maxDaysAtRisk
argument to the createStudyPopulation()
and createCreateStudyPopulationArgs()
functions.
Bug fixes:
Fixing IPTW.
Fixing error when stratifying and base population is empty (but overall population is not).
Changes:
Dropped insertDbPopulation()
function. This didn’t seem to be used by anyone, and would have required carrying the person ID throughout the pipeline.
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.
Adding log likelihood ratio to outcome model object.
Deprecating oracleTempSchema
argument in favor of tempEmulationSchema
in line with new SqlRender
interface.
Bug fixes:
Still was not always including the likelihood profile in the outcome model objects.
Fixing issues when IDs are integer64
.
Changes:
Bug fixes:
Fixing “argument ‘excludeDrugsFromCovariates’ is missing” error when calling createGetDbCohortMethodDataArgs()
without deprecated argument excludeDrugsFromCovariates
.
More testing and handling of empty exposure cohorts.
Fixing exclusion of covariate IDs when fitting propensity models.
Correct covariate balance computation when covariate values are integers.
Changes:
Bugfixes:
Changes:
Updating documentation: adding literature reference for IPTW, and using new SqlRender interface in vignettes.
Changing default equipoise bounds from 0.25-0.75 to 0.3-0.7 to be consistent with Alec Walker’s original paper.
Bugfixes:
Changes:
Added plotTimeToEvent function
Deprecating addExposureDaysToStart and addExposureDaysToEnd arguments, adding new arguments called startAnchor and endAnchor. The hope is this is less confusing.
Fixing random seeds for reproducibility.
Changing default equipoise bounds from 0.25-0.75 to 0.3-0.7 to be consistent with Alec Walker’s original paper.
Bugfixes:
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.
Correct calculation in original population count when using study end date.