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Changelog

Source: NEWS.md

gsm.kri v1.7.0

This minor release moves every gsm.viz-backed chart onto gsm.vizr: the vendored gsm.viz bundle and the legacy widget sources are gone, and the Premature Deaths and Eligibility bar charts render through gsm.vizr. The Premature Deaths randomization-to-death scatters stay on Plotly (#120).

Breaking Changes:

  • pd_BucketBar() is removed (#264) — the Plotly bucket bar, left without a caller once the Premature Deaths report moved to gsm.viz. Use pd_BucketBarSpec() with gsm.vizr::bars(). Its aggregation is now the new exported pd_BucketCounts(), which emits only the (group, category) pairs that occur (.drop = TRUE) rather than pd_BucketBar()’s complete grid, so an empty category carries no zero-count row and the dynamic category axis can thin.
  • gsm.kri now requires gsm.qtl (>= 1.4.0) for the gsm.vizr-backed eligibility charts, and takes a new dependency on gsm.vizr (>= 0.1.0).

Relocations to gsm.vizr:

  • The legacy widget wrappers (Widget_BarChart, Widget_ScatterPlot, Widget_TimeSeries, Widget_GroupOverview), their Shiny bindings, MakeChartConfig(), and the shared widget-control JS/CSS moved to gsm.vizr (#291). gsm.kri re-exports every name, so existing callers are unaffected. The vendored gsm.viz-2.4.1 bundle is retired; Widget_CrossStudyRiskScore now takes the bundle from gsm.vizr::html_dependency_gsm_viz().
  • The Premature Deaths bucket and reason barcharts render through gsm.vizr::bars() via the new pd_BucketBarSpec() / pd_BucketRows() / pd_ReasonBarSpec() / pd_ReasonRows() (#264, #288). The pilot wrappers Widget_PrematureDeathBucketBar() / Widget_PrematureDeathReasonBar() and their four Shiny bindings are removed; they were added after v1.6.1 and never shipped in a release. The hand-rolled count/percent toggle is replaced by gsm.viz’s native position toggle, and a missing OuterGroupID now serializes to a real null instead of the literal string "NA".
  • The Eligibility report’s 7 bar charts (Site, Country, Source, and the four Criteria/… tabs) render through gsm.qtl’s eligibility_groupBar() / eligibility_sourceBar() / criteria_groupBar() instead of plotly (#286). The separate “Site (by %)” tab is folded into the Site chart’s position toggle, matching the QTL report. Report_Eligibility.Rmd no longer loads ggplot2/plotly.

Other:

  • New update-gsm-viz-bundle skill under .github/skills/, referenced from AGENTS.md (#282). It documents how to re-vendor the gsm.viz assets in gsm.vizr from a release tag or a pinned upstream commit, and how to re-run gsm.kri’s bundle-regression browser spec afterwards. Repository tooling; not part of the installed package.
  • Repository links updated from Gilead-BioStats to Gilead-Public (#284). Two sets of Gilead-BioStats references are intentionally kept: the clindata link in README.md, because that repository has not moved, and the Gilead-BioStats/41 project board named by .github/CONTRIBUTING.md and the issue templates, which is org-level and shared with the other gsm packages.

gsm.kri v1.6.1

This patch release removes the log4r package dependency, because the log4r package was archived on CRAN (#262).

gsm.kri v1.6.0

This minor release introduces the Premature Deaths reporting module and adds cross-study sorting and filtering capabilities.

New Features:

  • Add Premature Deaths report module with interactive charts and patient listing (#221, #223)
    • Five-category classification of death timing via pd_Classify() (#246)
    • Bucket bar charts with count/percent toggle, on-bar labels, and range slider (#223, #246, #253)
    • Randomization-to-death scatter plot with fixed shared range across study/country/site views (#247)
    • Death-reason distribution chart with country-reactive filtering (#254)
    • Patient listing with site/country filter, eligibility status, and download button (#249)
    • Overview preamble with death-breakdown sub-line and ≤30 / 31–90 day split (#250, #252)
    • Sticky bucket-bar count/percent toggle and chip-strip filter UI (#253)
  • Add patient-level premature-death workflow pat0015 with configurable window (#221)
  • Derive Treatment Related status from deathcls + fatal related AE (#248)
  • Add eligibility status derivation via pd_EligibilityStatus() (#249, #250)
  • Add sort-by-enrollment option to Cross-Study Site Risk Score widget
  • Recalculate site metrics from the cross-study study filter selection

Bug Fixes:

  • Fix country cross-filter and absent country key guard in premature-death charts (#222)
  • Fix cou0015 to exclude subjects without a randomization date from the cohort (#247)
  • Fix plotly scalar-text bug by using customdata for hover tooltips
  • Remove risk score weight from cou0015 workflow
  • Fix overlapping sticky bucket toggle placement in report (#253)
  • Ignore inactive workflows (#237)

gsm.kri v1.5.2

This patch release fixes report display issues on the pkgdown site and renders missing examples.

Bug Fixes: - Fix overlapping summary table and text in Site/Country Report examples on the pkgdown site (#240) - Render missing pkgdown examples (#228)

gsm.kri v1.5.1

This patch release updates the GitHub action workflows to align with the new federated action framework in gsm.utils

gsm.kri v1.5.0

This minor release includes new workflows/tests and CI automation, plus performance-focused improvements to the qcthat testing infrastructure.

Changes: - Add test-data caching helpers and new tests (cache, pipe export, gt utilities), and refactor qual test data setup to use cached mapped data. - Introduce new “Deaths in First 90 Days / Premature Death” KRI workflows (site + country) and expand Cross-Study SRS widget study filtering to multi-select. - Migrate/replace qcthat GitHub Actions workflows.

gsm.kri v1.4.1

This patch release addresses the following issues:

  • Updates bug in cou0014 metric to use Identity method instead of Normal Approximation
  • Converts example R scripts to Rmd format with proper indexing for documentation using new gsm.utils implementation
  • Streamlines GitHub Actions workflow for releases

gsm.kri v1.4.0

This minor release updates the comprehensive site risk score (SRS) functionality in gsm.kri v1.4.0, including calculation methods, cross-study visualization capabilities, and extensive test coverage. Additionally, this release does the following: - Introduces new visualization widgets for time series, bar charts, and cross-study risk score display - Expands vignette documentation with detailed SRS methodology and implementation examples - Adds comprehensive test suite covering all KRI types with updated YAML workflow configurations - Adds new Inclusion/Exclusion Violation Rate KRI (0014)

gsm.kri 1.3.2

This patch release addresses a bug that was impacting the country-level KRI report.

gsm.kri 1.3.1

This patch release addresses a bug related to the gsm.viz implementation of site risk score.

gsm.kri 1.3.0

This release adds a new Site Risk Score metric that calculates weighted site-level risk across multiple KRIs. In short, the new default workflow has the following steps:

  • KRI Flags are given weights using the new RiskScoreWeight parameter in the yaml workflows for each KRI.
  • Site-level risk scores are calculated using the new CalculateRiskScore() function.
  • Site Risk Scores are saved in a new Metric srs0001 via a new standard workflow
  • A column showing site risk scores has been added to the KRI report via update in gsm.viz

See the new Site Risk Score vignette for full implementation details. Other minor updates are described below.

Minor Updates: - Update Issue Templates and Contributor Guidelines - Add GitHub Actions for tarball creation upon release

gsm.kri 1.2.2

This patch release fixes a bug in Report_KRI.Rmd that produced an error in LaTeX compilation of the report output.

gsm.kri 1.2.1

This patch release addresses changes to an .rda object updated in gsm.core v1.1.3.

gsm.kri 1.2.0

This minor release introduces new chart configuration functionality, refactors widget generation to support additional settings and unified output labels, and adds a new flag‐change report. Key changes:

  • Add MakeChartConfig() helper and propagate … into widgets and Visualize_Metric()
  • Refactor widgets to return a labeled lWidget with output_label attribute
  • Introduce Report_FlagChange() using updates from gsm.reporting v1.1.0

gsm.kri 1.1.2

This patch release updates the following yaml files in /2_metrics to update default accrual thresholds

  • kri0005.yaml
  • kri0006.yaml
  • kri0007.yaml
  • kri0008.yaml
  • kri0009.yaml
  • kri0010.yaml
  • kri0011.yaml
  • cou0005.yaml
  • cou0006.yaml
  • cou0007.yaml
  • cou0008.yaml
  • cou0009.yaml
  • cou0010.yaml
  • cou0011.yaml

gsm.kri 1.1.1

This patch release updates the description file to incorporate min version for gsm.core.

gsm.kri v1.1.0

This minor release adds a new KRI along with a few other small fixes.

  • PK Compliance Rate KRI workflows have been added as workflow 0013.
  • Remove unnecessary lower bound thresholds for the Data Quality KRIs.
  • All workflows now use the new FlagAccrual() functionality, so AccrualMetric and AccrualThreshold have been added to the meta of each yaml.

gsm.kri v1.0.0

We are happy to announce the first major release of the gsm.kri package, which houses the metric and module workflows, as well as all visualization functions and widgets for the GSM pipeline.

Key Enhancements:

  • Updated KRI Descriptions and Templates:
    The descriptions of Key Risk Indicators (KRIs) have been updated to improve clarity and understanding based on Risk Advisor feedback. PR #27

  • Qualification Report GitHub Actions (GHA):
    A new GitHub Actions workflow for generating qualification reports has been added, automating the process and ensuring better integration with the overall pipeline.
    PR #33

  • Update to gsm.viz 2.2:
    The package has been updated to use gsm.viz version 2.2, bringing new visualization capabilities and updates.
    PR #36

  • Replacement of clindata with gsm.datasim:
    In line with updates across other GSM packages, clindata has been replaced with the gsm.datasim package.
    PR #34

  • “How to Add a New KRI” Vignette:
    A new vignette has been added that provides a step-by-step guide on how to add a new KRI to the package, making it easier for users to extend and customize the package for their needs.
    PR #29

Other Updates:

  • Several bug fixes have been applied to improve stability and functionality.

For more detailed information, please refer to the pull requests linked above.

gsm.kri v0.0.1

This initial release migrates the KRI-specific functions, workflows, widgets and documentation from {gsm} to gsm.kri.