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.
What's Changed
- Main -> dev by Laura Maxwell (@lauramaxwell) in #189
- Allow Multiple study select by Jeremy Wildfire (@jwildfire) in #172
- Remove qual tests that have been moved to mapping, reporting and core. by Laura Maxwell (@lauramaxwell) in #179
- Auto-tag tests with issues by Jon Harmon (@jonthegeek) in #196
- Add new premature death KRIs by Laura Maxwell (@lauramaxwell) in #194
- Fix gsm.qtl@v1.2.0 by Zelos Zhu (@zdz2101) in #203
- gsm.kri v1.5.0 Release Candidate by Laura Maxwell (@lauramaxwell) in #198
- Update gsm.reporting remote to use main branch by Zelos Zhu (@zdz2101) in #204
Full Changelog: v1.4.1...v1.5.0
{qcthat} Reports
Milestone
⚠️ A qcthat issue test matrix with 1 milestone, 3 issues, and 6 tests
└─█─Milestone: v1.5.0 (3 issues, 6 tests)
├─☑️─Feature 193: Premature Deaths KRIs
│ └─✅─Qual: Given appropriate raw participant-level data, Deaths in First 90 Days assessment can be done using the Identity method (#193)
├─☑️─Technical Task 182: Cache test data
│ ├─✅─caching functions work correctly (#182)
│ ├─⚠️─cached mapped data is generated correctly (#182)
│ ├─✅─mapping output caching works (#182)
│ └─✅─cache clearing works (#182)
└─☑️─Feature 171: Filter on Multiple studies in Cross-study Site Risk Score Report
└─✅─Cross-study SRS report widget allows filtering on multiple studies (#171)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
🟢 All issues have at least one test
🙈 2 issues with label "qcthat-nocov" were ignored
Completed Issues
⚠️ A qcthat issue test matrix with 11 milestones, 49 issues, and 99 tests
├─█─Milestone: v1.0.0 (4 issues, 0 tests)
│ ├─☑️─Issue 37: Path to Report_KRI template
│ │ └─(no tests)
│ ├─☑️─Issue 35: Feature: Update gsm.viz js index
│ │ └─(no tests)
│ ├─☑️─Issue 30: Namespace all functions called in yaml workflows
│ │ └─(no tests)
│ └─☑️─Issue 1: Move Analyze, Transform, Flag, Summarize functions to gsm.kri
│ └─(no tests)
├─█─Milestone: v1.4.1 (3 issues, 1 test)
│ ├─☑️─Feature 184: Update example eligibility report.
│ │ └─(no tests)
│ ├─☑️─Bug 183: Align `cou0014` with `kri0014`.
│ │ └─✅─Qual: Given appropriate raw participant-level data, an Ineligibility Assessment can be done using the Identity method (#183)
│ └─☑️─Technical Task 161: Add qualification test for new ineligibility kri
│ └─(no tests)
├─█─Milestone: v1.5.0 (3 issues, 6 tests)
│ ├─☑️─Feature 193: Premature Deaths KRIs
│ │ └─✅─Qual: Given appropriate raw participant-level data, Deaths in First 90 Days assessment can be done using the Identity method (#193)
│ ├─☑️─Technical Task 182: Cache test data
│ │ ├─✅─caching functions work correctly (#182)
│ │ ├─⚠️─cached mapped data is generated correctly (#182)
│ │ ├─✅─mapping output caching works (#182)
│ │ └─✅─cache clearing works (#182)
│ └─☑️─Feature 171: Filter on Multiple studies in Cross-study Site Risk Score Report
│ └─✅─Cross-study SRS report widget allows filtering on multiple studies (#171)
├─█─Milestone: <none> (1 issue, 0 tests)
│ └─☑️─Requirement 168: Ineligibility accrual method should be `Numerator`.
│ └─(no tests)
├─█─Milestone: v1.1.0 (6 issues, 0 tests)
│ ├─☑️─Issue 45: Bugfix: Report pipeline failing to pick up functions
│ │ └─(no tests)
│ ├─☑️─Issue 32: Feature: Disable `MathJax` in KRI report.
│ │ └─(no tests)
│ ├─☑️─Issue 26: Feature: Add `nMinNumerator` to PK KRI.
│ │ └─(no tests)
│ ├─☑️─Issue 23: Feature: Update KRI descriptions
│ │ └─(no tests)
│ ├─☑️─Issue 11: Remove lower thresholds for Data Quality metrics
│ │ └─(no tests)
│ └─☑️─Issue 7: Feature: PK Compliance KRI
│ └─(no tests)
├─█─Milestone: v1.1.2 (2 issues, 0 tests)
│ ├─☑️─Requirement 74: Business Requirement: Update Accrual Thresholds for existing KRIs
│ │ └─(no tests)
│ └─☑️─Issue 68: Feature: Update lab and discontinuation KRI flag thresholds to only be positive z-scores
│ └─(no tests)
├─█─Milestone: v1.2.0 (8 issues, 9 tests)
│ ├─☑️─Issue 86: Bugfix: `GroupLabelKey` not found in new Flags Changed section of gsm.kri report
│ │ └─(no tests)
│ ├─☑️─Issue 80: Bugfix: `Report_KRI()` which renders `Report_KRI.Rmd` uses `add_Groups_metadata()` which isn't exported
│ │ └─(no tests)
│ ├─☑️─Issue 75: Feature: Add a list of flag changes from previous snapshot to report
│ │ ├─✅─returns NULL if required columns are missing (#75)
│ │ ├─✅─GroupLabel and MetricLabel default to IDs when missing (#75)
│ │ ├─✅─No output if only change is NA -> 0 (green) (#75)
│ │ └─✅─HTML output is generated for valid changed flags (#75)
│ ├─☑️─Issue 59: Feature: Align order of reporting data layer parameters across functions.
│ │ └─(no tests)
│ ├─☑️─Issue 57: Feature: Pass additional chart configuration via `...`.
│ │ └─(no tests)
│ ├─☑️─Issue 54: Feature: Add `chart_name` attribute in `Widget_*` functions.
│ │ └─(no tests)
│ ├─☑️─Issue 53: Feature: Generalize `Report_MetricCharts` to render any set of charts.
│ │ ├─✅─Handles all supported chart types (#53)
│ │ ├─✅─Handles some missing chart types (#53)
│ │ ├─✅─Handles empty input (#53)
│ │ ├─✅─Output formatting and no errors (#53)
│ │ └─✅─Handles missing output_label (#53)
│ └─☑️─Issue 47: Feature: Make log scale optional in scatter plot in support of PK visualization
│ └─(no tests)
├─█─Milestone: v1.2.2 (2 issues, 0 tests)
│ ├─☑️─Requirement 104: Business Requirement: Fix bugs related to pipeline and report output
│ │ └─(no tests)
│ └─☑️─Issue 103: Bugfix: LaTeX error in KRI Report
│ └─(no tests)
├─█─Milestone: v1.3.0 (8 issues, 0 tests)
│ ├─☑️─Feature 102: Incorporate site risk score into KRI report
│ │ └─(no tests)
│ ├─☑️─Technical Task 101: Create yaml for site risk score
│ │ └─(no tests)
│ ├─☑️─Requirement 98: Implement Site Risk Scores
│ │ └─(no tests)
│ ├─☑️─Feature 97: Add report component that tabulates risk signal weights.
│ │ └─(no tests)
│ ├─☑️─Technical Task 96: Add supplemental metric data domain that captures risk signal weights.
│ │ └─(no tests)
│ ├─☑️─Technical Task 70: Calculate Site Risk Score as new Metric
│ │ └─(no tests)
│ ├─☑️─Requirement 65: Basic Site Risk Score Prototype
│ │ └─(no tests)
│ └─☑️─Requirement 63: ePRO Compliance KRI - Proof of Concept
│ └─(no tests)
├─█─Milestone: v1.3.1 (1 issue, 0 tests)
│ └─☑️─Bug 118: `Widget_GroupOverview` displays mock site risk score data when site risk score is absent in data.
│ └─(no tests)
├─█─Milestone: v1.3.2 (1 issue, 2 tests)
│ └─☑️─Bug 125: Country-level report is broken.
│ ├─✅─Widget_GroupOverview returns expected data (#125)
│ └─✅─Widget_GroupOverview uses correct Group or errors out when strGroupLevel is NULL (#125)
└─█─Milestone: v1.4.0 (10 issues, 81 tests)
├─☑️─Feature 166: Parametrize options for addOutcomeSelect
│ ├─✅─Widget_BarChart creates a valid HTML widget {#166}
│ ├─✅─Widget_BarChart works with custom vOutcomeOptions {#166}
│ ├─✅─Widget_BarChart assertions work {#166}
│ ├─✅─Widget_TimeSeries creates a valid HTML widget {#166}
│ ├─✅─Widget_TimeSeries works with custom vOutcomeOptions {#166}
│ └─✅─Widget_TimeSeries assertions work {#166}
├─☑️─Feature 71: Create a cross-study KRI report
│ ├─✅─Returns correct structure with required columns (#71, #144)
│ ├─✅─Calculates metrics correctly for multiple studies (#71, #144)
│ ├─✅─Sorts by average risk score descending (#71, #144)
│ ├─✅─Works with single study per site (#71, #144)
│ ├─✅─Adds InvestigatorName when dfGroups provided (#71, #144)
│ ├─✅─Handles multiple investigator names per site (#71, #144)
│ ├─✅─Handles missing columns in dfGroups gracefully (#71, #144)
│ ├─✅─Respects strGroupLevel parameter (#71, #144)
│ ├─✅─Errors when no data for specified GroupLevel (#71, #144)
│ ├─✅─Returns empty data frame when Analysis_srs0001 not present (#71, #144)
│ ├─✅─Validates input types (#71, #144)
│ ├─✅─Works with custom strNameCol parameter (#71, #144)
│ ├─✅─Widget_CrossStudyRiskScore creates an htmlwidget (#71)
│ ├─✅─Widget_CrossStudyRiskScore errors if Analysis_srs0001 is missing (#71)
│ └─✅─Widget_CrossStudyRiskScore validates inputs (#71)
├─☑️─Technical Task 162: Implement gsm.utils v0.2.0 workflows
│ └─(no tests)
├─☑️─Technical Task 159: Add Qualification Tests for existing Functionality
│ ├─✅─Qual: Given appropriate raw participant-level data, a Data Change Rate Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Data Change Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Data Entry Lag Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Data Entry Lag Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Query Age Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Query Age Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Query Rate Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Query Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a PK Compliance Assessment can be done using the Identity method (#159)
│ ├─✅─Qual: PK Compliance Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable (#159)
│ ├─✅─Qual: Given summarized analytics data, all appropriate aspects of site risk score are available to calculate it correctly (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, an Adverse Event Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Adverse Event Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Protocol Deviation Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Protocol Deviation Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Dispositon Assessment can be done using the Normal Approximation method (#159)
│ ├─✅─Qual: Disposition Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable (#159)
│ ├─✅─Qual: Given appropriate raw participant-level data, a Labs Assessment can be done using the Normal Approximation method (#159)
│ └─✅─Qual: Labs Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable (#159)
├─☑️─Feature 157: Incorpoate `IE` into standard site-based KRI
│ └─✅─Ensure report renders normally {#157}
├─☑️─Technical Task 145: Remove test noise
│ └─✅─Widget_GroupOverview creates a valid HTML widget (#145)
├─☑️─Technical Task 144: Add unit tests for SummarizeCrossStudy()
│ ├─✅─Returns correct structure with required columns (#71, #144)
│ ├─✅─Calculates metrics correctly for multiple studies (#71, #144)
│ ├─✅─Sorts by average risk score descending (#71, #144)
│ ├─✅─Works with single study per site (#71, #144)
│ ├─✅─Adds InvestigatorName when dfGroups provided (#71, #144)
│ ├─✅─Handles multiple investigator names per site (#71, #144)
│ ├─✅─Handles missing columns in dfGroups gracefully (#71, #144)
│ ├─✅─Respects strGroupLevel parameter (#71, #144)
│ ├─✅─Errors when no data for specified GroupLevel (#71, #144)
│ ├─✅─Returns empty data frame when Analysis_srs0001 not present (#71, #144)
│ ├─✅─Validates input types (#71, #144)
│ └─✅─Works with custom strNameCol parameter (#71, #144)
├─☑️─Technical Task 135: Add `MakeWeights` helper function
│ ├─✅─MakeWeights returns correct structure (#135)
│ ├─✅─MakeWeights parses comma-separated values correctly (#135)
│ ├─✅─MakeWeights calculates WeightMax correctly (#135)
│ ├─✅─MakeWeights handles multiple metrics (#135)
│ ├─✅─MakeWeights validates required columns (#135)
│ ├─✅─MakeWeights filters out NA values (#135)
│ ├─✅─MakeWeights handles empty data after filtering NAs (#135)
│ ├─✅─MakeWeights handles single flag-weight pair (#135)
│ ├─✅─MakeWeights handles zero weights (#135)
│ ├─✅─MakeWeights handles negative flags (#135)
│ ├─✅─MakeWeights handles large numbers (#135)
│ ├─✅─MakeWeights handles decimal weights (#135)
│ ├─✅─MakeWeights output can be joined to results data (#135)
│ ├─✅─MakeWeights works with gsm.core::reportingMetrics (#135)
│ ├─✅─MakeWeights handles symmetric weights correctly (#135)
│ ├─✅─MakeWeights handles asymmetric weights correctly (#135)
│ ├─✅─MakeWeights detects mismatched Flag and RiskScoreWeight lengths (#135)
│ ├─✅─MakeWeights detects mismatched lengths with multiple metrics (#135)
│ ├─✅─MakeWeights detects fewer weights than flags (#135)
│ ├─✅─MakeWeights detects more weights than flags (#135)
│ └─✅─MakeWeights succeeds when all lengths match (#135)
├─☑️─Technical Task 127: Require `CalculateRiskScore` to run separately for each snapshot/study
│ ├─✅─CalculateRiskScore returns correct structure (#127)
│ ├─✅─CalculateRiskScore calculates risk scores correctly (#127)
│ ├─✅─CalculateRiskScore handles custom MetricID (#127)
│ ├─✅─CalculateRiskScore validates required columns in dfResults (#127)
│ ├─✅─CalculateRiskScore validates required columns in dfWeights (#127)
│ ├─✅─CalculateRiskScore validates MetricID uniqueness (#127)
│ ├─✅─CalculateRiskScore validates numeric Weight and WeightMax (#127)
│ ├─✅─CalculateRiskScore validates unique combinations (#127)
│ ├─✅─CalculateRiskScore validates consistent WeightMax per MetricID (#127)
│ ├─✅─CalculateRiskScore handles NA values with warning (#127)
│ ├─✅─CalculateRiskScore works with all NA weights for a group (#127)
│ ├─✅─CalculateRiskScore handles single row input (#127)
│ ├─✅─CalculateRiskScore handles zero weights (#127)
│ ├─✅─CalculateRiskScore handles large numbers (#127)
│ ├─✅─CalculateRiskScore aggregates weights correctly across metrics (#127)
│ └─✅─CalculateRiskScore handles multiple group levels (#127)
└─☑️─Bug 107: The metric table in the KRI report occasionally displays "metricTable" instead of "Metric Table".
├─✅─output_label attribute is set even with no flags (Issue #107)
└─✅─Output is expected object (#107)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
⭕ 33 issues lack tests
🙈 25 issues with label "qcthat-nocov" were ignored; 1 issue with label "qcthat-uat" was ignored
This report was generated by this GitHub Actions run.
Last updated: 2026-04-17 19:46:46 UTC
Session Info
─ Session info ───────────────────────────────────────────────────────────────setting value
version R version 4.5.3 (2026-03-11)
os Ubuntu 24.04.4 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate C.UTF-8
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date 2026-04-17
pandoc 3.1.3 @ /usr/bin/pandoc
quarto NA
─ Packages ───────────────────────────────────────────────────────────────────
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pkgload 1.5.1 2026-04-01 [1] RSPM
plotly 4.12.0 2026-01-24 [1] RSPM
praise 1.0.0 2015-08-11 [1] RSPM
processx 3.8.7 2026-04-01 [1] RSPM
promises 1.5.0 2025-11-01 [1] RSPM
ps 1.9.2 2026-03-31 [1] RSPM
purrr 1.2.2 2026-04-10 [1] RSPM
qcthat 1.1.2 2026-04-17 [1] Github (Gilead-Public/qcthat@d0958dc)
R6 2.6.1 2025-02-15 [1] RSPM
rappdirs 0.3.4 2026-01-17 [1] RSPM
RColorBrewer 1.1-3 2022-04-03 [1] RSPM
Rcpp 1.1.1-1 2026-04-16 [1] RSPM
reactable 0.4.5 2025-12-01 [1] RSPM
reactR 0.6.1 2024-09-14 [1] RSPM
rex 1.2.2 2026-03-28 [1] RSPM
rlang 1.2.0 2026-04-06 [1] RSPM
rmarkdown 2.31 2026-03-26 [1] RSPM
rpart 4.1.24 2025-01-07 [3] CRAN (R 4.5.3)
rprojroot 2.1.1 2025-08-26 [1] RSPM
rrapply 1.2.8 2025-11-25 [1] RSPM
rstudioapi 0.18.0 2026-01-16 [1] RSPM
S7 0.2.1-1 2025-11-14 [1] RSPM
sass 0.4.10 2025-04-11 [1] RSPM
scales 1.4.0 2025-04-24 [1] RSPM
sessioninfo 1.2.3 2025-02-05 [1] RSPM
spatial 7.3-18 2025-01-01 [3] CRAN (R 4.5.3)
splines 4.5.3 2026-03-11 [3] local
stats * 4.5.3 2026-03-11 [3] local
stats4 4.5.3 2026-03-11 [3] local
stringi 1.8.7 2025-03-27 [1] RSPM
stringr 1.6.0 2025-11-04 [1] RSPM
survival 3.8-6 2026-01-16 [3] CRAN (R 4.5.3)
sys 3.4.3 2024-10-04 [1] RSPM
tcltk 4.5.3 2026-03-11 [3] local
testthat 3.3.2 2026-01-11 [1] RSPM
tibble 3.3.1 2026-01-11 [1] RSPM
tidyr 1.3.2 2025-12-19 [1] RSPM
tidyselect 1.2.1 2024-03-11 [1] RSPM
timechange 0.4.0 2026-01-29 [1] RSPM
tinytex 0.59 2026-03-28 [1] RSPM
tools 4.5.3 2026-03-11 [3] local
usethis 3.2.1 2025-09-06 [1] RSPM
utf8 1.2.6 2025-06-08 [1] RSPM
utils * 4.5.3 2026-03-11 [3] local
V8 8.1.0 2026-04-12 [1] RSPM
vctrs 0.7.3 2026-04-11 [1] RSPM
viridisLite 0.4.3 2026-02-04 [1] RSPM
waldo 0.6.2 2025-07-11 [1] RSPM
whisker 0.4.1 2022-12-05 [1] RSPM
withr 3.0.2 2024-10-28 [1] RSPM
xfun 0.57 2026-03-20 [1] RSPM
xml2 1.5.2 2026-01-17 [1] RSPM
yaml 2.3.12 2025-12-10 [1] RSPM
zip 2.3.3 2025-05-13 [1] RSPM
[1] /home/runner/work/_temp/Library
[2] /opt/R/4.5.3/lib/R/site-library
[3] /opt/R/4.5.3/lib/R/library
- ── Packages attached to the search path.
──────────────────────────────────────────────────────────────────────────────
