gsm.qtl v1.2.0

Bug Fixes:

Fixed issue #90: Updated eligibility_groupBar(), discontinuation_groupBar(), and reasons_groupBar() to accept separate dfNum/dfDenom inputs, correcting count alignment for discontinued and ineligible participants.
Fixed footnote rendering logic so footnotes always display in report charts.

Key Enhancements:

Added bSwapAxes parameter to criteria_groupBar() to support swapped axis views (Site/Criteria and Country/Criteria tabs).
Added calc_plotly_footnote_layout() utility for consistent plotly footnote positioning across charts.
Removed completed/ongoing categories from reasons bar charts to focus on actionable discontinuation reasons.
Fully namespaced all function calls in QTL report templates (QTL0001.Rmd, QTL0002.Rmd, Report_QTL.Rmd) with gsm.qtl:: prefix.
Expanded test coverage for eligibility, analysis utilities, and QTL reporting.

{qcthat} Reports

Milestone

✅ A qcthat issue test matrix with 1 milestone, 7 issues, and 13 tests

└─█─Milestone: v1.2.0 (7 issues, 13 tests)
  ├─☑️─Bug 90: QTL0001 Criteria by site/country barcharts are broken/too zoomed in
  │ ├─✅─calc_plotly_footnote_layout expands bottom margin for wrapped footnotes (#90)
  │ ├─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
  │ ├─✅─reasons_groupBar swaps axes correctly when bSwapAxes is TRUE (#90)
  │ ├─✅─eligibility_groupBar reserves space when a footnote is present (#90)
  │ ├─✅─criteria_groupBar uses grouping and label arguments correctly when swapping axes (#90)
  │ └─✅─Example QTL Report for 2026Q1 meets ui/ux/aesthetics expectations (#90)
  ├─☑️─Requirement 84: QTL Tabletop Immediately Addressable feedback
  │ ├─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
  │ └─✅─QTL_lineplot_v2 validates required arguments (#49, #84)
  ├─☑️─Feature 80: Test suite is lacking
  │ ├─✅─Analyze_OneSideProp validates nPropRate argument bounds (#80)
  │ ├─✅─calc_fig_size covers n_rows, base, and per arguments (#80)
  │ ├─✅─ResultsProcessor uses dfResults and dfMetrics arguments (#80)
  │ └─✅─QTL_lineplot uses dfResults and strQTL arguments (#80)
  ├─☑️─Bug 76: `discontinuation_groupBar` hard-codes `compyn=='N'` to study discontinuation.
  │ └─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
  ├─☑️─Bug 70: Address found bugs from eligibility report meeting
  │ └─✅─Eligibility_Overview uses all arguments (#21, #22, #70)
  ├─☑️─Feature 49: Implement Custom Time Series Widget for QTL 
  │ ├─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
  │ └─✅─QTL_lineplot_v2 validates required arguments (#49, #84)
  └─☑️─Feature 27: Optimize Time Series Chart for its respective axis, fix legend, revisit JS?
    └─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped

✅ All tests passed

🟢 All issues have at least one test

🙈 8 issues with label "qcthat-nocov" were ignored; 1 issue with label "qcthat-uat" was ignored

Completed Issues

🚫 A qcthat issue test matrix with 4 milestones, 29 issues, and 35 tests

├─█─Milestone: v0.1.0 (15 issues, 22 tests)
│ ├─☑️─Issue 30: Feature: Figure out how to conditionally run child .Rmd
│ │ ├─🚫─Report_QTL renders a valid HTML report for full metric input (#4, #9, #19, #30, #35)
│ │ └─🚫─Report_QTL renders a valid HTML report for single metric input (#4, #9, #19, #30)
│ ├─☑️─Feature 11: Feature: Write function(s) that generate dynamic threshold for Eligibility QTL
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #46)
│ │ ├─✅─Analyze One Side Prop works for Study, when nPropRate is the same (#5, #11, #46)
│ │ ├─✅─Analyze_OneSideProp handles required and optional arguments (#5, #11, #46)
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73)
│ │ └─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ ├─☑️─Feature 9: Feature: QTL report
│ │ ├─✅─QTL_Overview uses all arguments (#4, #9)
│ │ ├─✅─Report_QTL validates required structures (#4, #9, #19)
│ │ ├─✅─Report_QTL passes arguments to render (#4, #9, #19)
│ │ ├─🚫─Report_QTL renders a valid HTML report for full metric input (#4, #9, #19, #30, #35)
│ │ └─🚫─Report_QTL renders a valid HTML report for single metric input (#4, #9, #19, #30)
│ ├─☑️─Feature 5: Add basic workflow for Eligibility metric
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #46)
│ │ ├─✅─Analyze One Side Prop works for Study, when nPropRate is the same (#5, #11, #46)
│ │ ├─✅─Analyze_OneSideProp handles required and optional arguments (#5, #11, #46)
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73)
│ │ └─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ ├─☑️─Requirement 4: Business Requirement: QTL Metrics/Report Prototype
│ │ ├─✅─QTL_Overview uses all arguments (#4, #9)
│ │ ├─✅─Report_QTL validates required structures (#4, #9, #19)
│ │ ├─✅─Report_QTL passes arguments to render (#4, #9, #19)
│ │ ├─🚫─Report_QTL renders a valid HTML report for full metric input (#4, #9, #19, #30, #35)
│ │ └─🚫─Report_QTL renders a valid HTML report for single metric input (#4, #9, #19, #30)
│ ├─☑️─Issue 3: Feature: Treatment Discontinuation
│ │ └─✅─Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73)
│ ├─☑️─Issue 2: Feature: Eligibility domains mapping
│ │ └─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ ├─☑️─Issue 24: Make the Listing exportable - either as a separate report or via a csv download in the report
│ │ └─✅─eligibility_listing covers df and download arguments (#21, #22, #24, #25)
│ ├─☑️─Requirement 23: Business Requirement: Update criteria bar charts to include multiple criteria for participants with multiple ineligibility reasons.
│ │ └─✅─criteria_groupBar uses grouping and label arguments (#14, #21, #22, #23)
│ ├─☑️─Issue 22: Feature: Visualization Wrappers
│ │ ├─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
│ │ ├─✅─discontinuation_reasonBar uses df and reason variable (#14, #21, #22)
│ │ ├─✅─reasons_groupBar uses group and reason arguments (#14, #21, #22)
│ │ ├─✅─discontinuation_map_reasons respects yaml_path (#21, #22)
│ │ ├─✅─eligibility_groupBar uses all arguments (#14, #15, #21, #22, #60)
│ │ ├─✅─eligibility_sourceBar returns plotly object (#14, #21, #22)
│ │ ├─✅─criteria_groupBar uses grouping and label arguments (#14, #21, #22, #23)
│ │ ├─✅─eligibility_listing covers df and download arguments (#21, #22, #24, #25)
│ │ ├─✅─scrollable_gt uses height and width arguments (#21, #22)
│ │ └─✅─Eligibility_Overview uses all arguments (#21, #22, #70)
│ ├─☑️─Issue 21: Feature: QTL Study Discontinuation
│ │ ├─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
│ │ ├─✅─discontinuation_reasonBar uses df and reason variable (#14, #21, #22)
│ │ ├─✅─reasons_groupBar uses group and reason arguments (#14, #21, #22)
│ │ ├─✅─discontinuation_map_reasons respects yaml_path (#21, #22)
│ │ ├─✅─eligibility_groupBar uses all arguments (#14, #15, #21, #22, #60)
│ │ ├─✅─eligibility_sourceBar returns plotly object (#14, #21, #22)
│ │ ├─✅─criteria_groupBar uses grouping and label arguments (#14, #21, #22, #23)
│ │ ├─✅─eligibility_listing covers df and download arguments (#21, #22, #24, #25)
│ │ ├─✅─scrollable_gt uses height and width arguments (#21, #22)
│ │ ├─✅─Eligibility_Overview uses all arguments (#21, #22, #70)
│ │ └─✅─Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73)
│ ├─☑️─Issue 19: Feature: Polish Report
│ │ ├─✅─Report_QTL validates required structures (#4, #9, #19)
│ │ ├─✅─Report_QTL passes arguments to render (#4, #9, #19)
│ │ ├─🚫─Report_QTL renders a valid HTML report for full metric input (#4, #9, #19, #30, #35)
│ │ └─🚫─Report_QTL renders a valid HTML report for single metric input (#4, #9, #19, #30)
│ ├─☑️─Issue 17: Feature: Add mapping file for `Mapped_Exclusion`
│ │ └─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ ├─☑️─Issue 16: Feature: Add horizontal line at I/E target
│ │ └─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
│ └─☑️─Issue 14: Feature: Generate Bar Charts based on multiple categorization
│   ├─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
│   ├─✅─discontinuation_reasonBar uses df and reason variable (#14, #21, #22)
│   ├─✅─reasons_groupBar uses group and reason arguments (#14, #21, #22)
│   ├─✅─eligibility_groupBar uses all arguments (#14, #15, #21, #22, #60)
│   ├─✅─eligibility_sourceBar returns plotly object (#14, #21, #22)
│   └─✅─criteria_groupBar uses grouping and label arguments (#14, #21, #22, #23)
├─█─Milestone: v1.0.0 (6 issues, 8 tests)
│ ├─☑️─Requirement 50: Prepare `gsm.qtl` for Q3 release
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73)
│ │ ├─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ │ └─✅─Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73)
│ ├─☑️─Bug 46: Bugfix: Calculation of upper funnel bug
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #46)
│ │ ├─✅─Analyze One Side Prop works for Study, when nPropRate is the same (#5, #11, #46)
│ │ └─✅─Analyze_OneSideProp handles required and optional arguments (#5, #11, #46)
│ ├─☑️─Issue 42: QC: Create qualification framework and tests
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73)
│ │ ├─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ │ └─✅─Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73)
│ ├─☑️─Requirement 39: Qualify QTL Metrics
│ │ ├─✅─Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73)
│ │ ├─✅─Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73)
│ │ └─✅─Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73)
│ ├─☑️─Issue 35: Feature: Add more columns to the discontinuation listing in QTL0002
│ │ └─🚫─Report_QTL renders a valid HTML report for full metric input (#4, #9, #19, #30, #35)
│ └─☑️─Feature 25: Make I/E listing exportable
│   └─✅─eligibility_listing covers df and download arguments (#21, #22, #24, #25)
├─█─Milestone: v1.1.0 (1 issue, 4 tests)
│ └─☑️─Feature 60: Add a percentage based barplot for Ineligibiltiy Report
│   ├─✅─eligibility_groupBar uses all arguments (#14, #15, #21, #22, #60)
│   ├─✅─eligibility_groupBar bPercentage = FALSE shows counts (#60)
│   ├─✅─eligibility_groupBar bPercentage = TRUE shows percentages (#60)
│   └─✅─eligibility_groupBar bPercentage TRUE uses stacked fill position (#60)
└─█─Milestone: v1.2.0 (7 issues, 13 tests)
  ├─☑️─Bug 90: QTL0001 Criteria by site/country barcharts are broken/too zoomed in
  │ ├─✅─calc_plotly_footnote_layout expands bottom margin for wrapped footnotes (#90)
  │ ├─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
  │ ├─✅─reasons_groupBar swaps axes correctly when bSwapAxes is TRUE (#90)
  │ ├─✅─eligibility_groupBar reserves space when a footnote is present (#90)
  │ ├─✅─criteria_groupBar uses grouping and label arguments correctly when swapping axes (#90)
  │ └─✅─Example QTL Report for 2026Q1 meets ui/ux/aesthetics expectations (#90)
  ├─☑️─Requirement 84: QTL Tabletop Immediately Addressable feedback
  │ ├─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
  │ └─✅─QTL_lineplot_v2 validates required arguments (#49, #84)
  ├─☑️─Feature 80: Test suite is lacking
  │ ├─✅─Analyze_OneSideProp validates nPropRate argument bounds (#80)
  │ ├─✅─calc_fig_size covers n_rows, base, and per arguments (#80)
  │ ├─✅─ResultsProcessor uses dfResults and dfMetrics arguments (#80)
  │ └─✅─QTL_lineplot uses dfResults and strQTL arguments (#80)
  ├─☑️─Bug 76: `discontinuation_groupBar` hard-codes `compyn=='N'` to study discontinuation.
  │ └─✅─discontinuation_groupBar uses all arguments (#14, #21, #22, #76, #90)
  ├─☑️─Bug 70: Address found bugs from eligibility report meeting
  │ └─✅─Eligibility_Overview uses all arguments (#21, #22, #70)
  ├─☑️─Feature 49: Implement Custom Time Series Widget for QTL 
  │ ├─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
  │ └─✅─QTL_lineplot_v2 validates required arguments (#49, #84)
  └─☑️─Feature 27: Optimize Time Series Chart for its respective axis, fix legend, revisit JS?
    └─✅─QTL_lineplot_v2 returns timeseries widget with threshold flags (#16, #27, #49, #84)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped

🚫 2 tests were skipped

🟢 All issues have at least one test

🙈 16 issues with label "qcthat-nocov" were ignored; 4 issues with label "qcthat-uat" were ignored

This report was generated by this GitHub Actions run.

Last updated: 2026-04-17 16:05:13 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

ctype C.UTF-8

tz UTC

date 2026-04-17

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

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qcthat 1.1.2 2026-04-17 [1] Github (Gilead-Public/qcthat@d0958dc)

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

rcmdcheck 1.4.0 2021-09-27 [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

riskmetric 0.2.7 2026-04-01 [1] RSPM

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 7.3.3 2025-09-03 [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

rversions 3.0.0 2025-10-09 [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

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [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

systemfonts 1.3.2 2026-03-05 [1] RSPM

tcltk 4.5.3 2026-03-11 [3] local

testthat 3.3.2 2026-01-11 [1] RSPM

textshaping 1.0.5 2026-03-06 [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

triebeard 0.4.1 2023-03-04 [1] RSPM

urlchecker 1.0.1 2021-11-30 [1] RSPM

urltools 1.7.3.1 2025-06-12 [1] RSPM

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

xopen 1.0.1 2024-04-25 [1] RSPM

xtable 1.8-8 2026-02-22 [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

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gsm.qtl v1.2.0

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