Qualification Report for {gsm.qtl} R Package
Report Run Date: 2026-09-09
Source:vignettes/articles/Qualification.Rmd
Qualification.RmdIntroduction
Risk-Based Quality Monitoring (RBQM) is a proactive approach to clinical trial monitoring that focuses on identifying and addressing the most critical risks to the integrity of study data and patient safety. This approach aims to ensure that study data are accurate, reliable, and credible while optimizing the use of resources and minimizing the burden on study sites.
The {gsm} suite of R packages supports RBQM by
performing risk assessments primarily focused on detecting differences
in quality at the site level. This approach is intended to detect
potential issues related to critical data or process(es) across the
major risk categories of safety, efficacy, disposition, treatment, and
general quality. Each category consists of one or more risk
assessment(s). Each risk assessment analyzes the data to flag sites with
potential outliers and provides a visualization to help the user
understand the issue.
Scope
Qualification testing ensures that core functions execute as expected
on a system-wide scale. Qualification includes executing various
functional, performance, and usability testing. Qualification tests are
designed to provide developers with a repeatable process that is easy to
update and document. This document summarizes the qualification testing
performed on gsm functions essential to the analysis
workflow.
Process Overview
Each essential gsm workflow function is independently
qualified using specifications and test cases compiled in this report.
Details are provided below.
Specifications
Specifications capture the most critical use cases for a given function. Each function must have at least one (1) specification, and each specification must have at least one (1) associated test case. Multiple specifications may exist for a function, and multiple test cases may exist for a specification.
Each specification includes the following components:
Description: outlines the use case for the specification
Risk Assessment
Risk Level: assigned a value of “Low”, “Medium”, or “High”, corresponding to the risk associated with the specification failing
Risk Impact: assigned a value of “Low”, “Medium”, or “High”, corresponding to the severity of the impact associated with the specification failing
Test Cases: lists measurable test cases associated with the specification
| Spec ID | Spec Description | Risk | Impact | Associated Test IDs |
|---|---|---|---|---|
| S1_1 | Given a thresold and multiplier, function can appropriately calculate an upper funnel metric for comparison | High | High | T1_1 |
| S2_1 | Given appropriate raw participant-level data, an Ineligibility Assessment can be done using methods cited in gsm.qtl | High | High | T2_1 |
| S3_1 | Given appropriate raw participant-level data, an Early Discontinuation Assessment can be done using methods cited in gsm.qtl | High | High | T3_1 |
One Row Per Test
| Function | Spec ID | Test ID | Test Description | Test Result |
|---|---|---|---|---|
| One Side Prop unit test | S1_1 | T1_1 | Analyze One Side Prop works for Study, when nProRate is clearly violated (#5, #11, #39, #42, #50, #73) | Pass |
| Ineligibility Assessment | S2_1 | T2_1 | Given appropriate inclusion/exclusion related data, calculates appropriate QTL threshold. (#2, #5, #11, #17, #39, #42, #50, #73) | Pass |
| Early Discontinuation Assessment | S3_1 | T3_1 | Given appropriate study discontinuation related data, calculates appropriate QTL threshold. (#3, #21, #39, #42, #50, #73) | Pass |
Qualification Testing Environment
Session Information
R version 4.6.1 (2026-06-24)
Platform: x86_64-pc-linux-gnu
locale: LC_CTYPE=C.UTF-8, LC_NUMERIC=C, LC_TIME=C.UTF-8, LC_COLLATE=C.UTF-8, LC_MONETARY=C.UTF-8, LC_MESSAGES=C.UTF-8, LC_PAPER=C.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=C.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: gsm.qtl(v.1.4.0), testthat(v.3.3.2), stringr(v.1.6.0), gh(v.1.6.1.9000), pander(v.0.6.6), purrr(v.1.2.2), dplyr(v.1.2.1), knitr(v.1.52), gt(v.1.3.0) and gsm.core(v.1.3.1)
loaded via a namespace (and not attached): gtable(v.0.3.6), xfun(v.0.60), bslib(v.0.12.0), ggplot2(v.4.0.3), htmlwidgets(v.1.6.4), devtools(v.2.5.2), vctrs(v.0.7.3), tools(v.4.6.1), generics(v.0.1.4), tibble(v.3.3.1), pkgconfig(v.2.0.3), data.table(v.1.18.6.1), RColorBrewer(v.1.1-3), S7(v.0.2.2), desc(v.1.4.3), lifecycle(v.1.0.5), compiler(v.4.6.1), farver(v.2.1.2), textshaping(v.1.0.5), brio(v.1.1.5), htmltools(v.0.5.9), usethis(v.3.2.1), sass(v.0.4.10), yaml(v.2.3.12), plotly(v.4.12.1), gsm.vizr(v.0.1.0), pillar(v.1.11.1), pkgdown(v.2.2.1), jquerylib(v.0.1.4), tidyr(v.1.3.2), ellipsis(v.0.3.3), cachem(v.1.1.0), sessioninfo(v.1.2.4), tidyselect(v.1.2.1), digest(v.0.6.39), stringi(v.1.8.9), duckdb(v.1.5.5), forcats(v.1.0.1), rprojroot(v.2.1.1), fastmap(v.1.2.0), grid(v.4.6.1), here(v.1.0.2), cli(v.3.6.6), magrittr(v.2.0.5), pkgbuild(v.1.4.8), withr(v.3.0.3), waldo(v.0.6.2), scales(v.1.4.0), rmarkdown(v.2.32), httr(v.1.4.9), otel(v.0.2.0), ragg(v.1.5.2), memoise(v.2.0.1), evaluate(v.1.0.5), viridisLite(v.0.4.3), rlang(v.1.3.0), Rcpp(v.1.1.2), DBI(v.1.3.0), glue(v.1.8.1), workr(v.1.1.0), xml2(v.1.6.0), pkgload(v.1.5.3), rstudioapi(v.0.19.0), jsonlite(v.2.0.0), R6(v.2.6.1), systemfonts(v.1.3.2) and fs(v.2.1.0)
Pull Request History
The GitHub Pull Request (PR) process begins with the creation of one
or more issues that clearly define the proposed additions or revisions
to the package. Each issue should be assigned to a product developer
(PD) who then creates a fix branch named according to the
related issue(s), and implements the necessary code updates. Once the
work is complete, the PD opens a Pull Request to merge the
fix branch into the target branch (typically the
dev branch). They must assign the PR to themselves, request
one or more reviewers, and link the PR to the associated issue(s).
Before the fix branch can be merged, the PR must be approved by the
designated reviewers and pass all required GitHub qualification checks.
Once these conditions are met, the fix branch is merged
into the target branch. This process is fully documented in the Contributor
Guidelines
Below, the most recent 10 PRs into gsm.qtl are displayed. See all Pull Requests here.
Pull Request 138: gsm.qtl v1.4.0 Release
Merging release-1.4.0 into main
https://github.com/Gilead-Public/gsm.qtl/pull/138
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| michkam89 | 2026-08-26 12:08:48 | copilot-pull-request-reviewer[bot] michkam89 nandriychuk samussiah | COMMENTED |
Pull Request 137: Migrate QTL report barcharts to gsm.vizr (#134)
Merging feat/134-bars-migration into dev
https://github.com/Gilead-Public/gsm.qtl/pull/137
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| michkam89 | 2026-08-13 14:49:11 | copilot-pull-request-reviewer[bot] michkam89 samussiah | COMMENTED |
Pull Request 136: Ignore data-raw
Merging ignore-data-raw into dev
https://github.com/Gilead-Public/gsm.qtl/pull/136
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| jharmon-gilead | 2026-08-13 14:37:12 | lauramaxwell | APPROVED |
Pull Request 133: fix: update Gilead-BioStats links to Gilead-Public
Merging fix-132 into dev
https://github.com/Gilead-Public/gsm.qtl/pull/133
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| nandriychuk | 2026-08-11 18:12:35 | jharmon-gilead | APPROVED |
Pull Request 131: Use public actions
Merging public-actions into dev
https://github.com/Gilead-Public/gsm.qtl/pull/131
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| jharmon-gilead | 2026-08-04 15:41:12 | nandriychuk | APPROVED |
Pull Request 127: Fix 124: Remove unused riskmetric package
Merging remove-riskmetric into dev
https://github.com/Gilead-Public/gsm.qtl/pull/127
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| jharmon-gilead | 2026-07-21 17:04:08 | zdz2101 | APPROVED |
Pull Request 126: Main -> dev
Merging main into dev
https://github.com/Gilead-Public/gsm.qtl/pull/126
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| lauramaxwell | 2026-07-17 19:14:00 | jharmon-gilead | APPROVED |
Pull Request 123: Release candidate v1.3.0
Merging rc-v1.3.0 into main
https://github.com/Gilead-Public/gsm.qtl/pull/123
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| lauramaxwell | 2026-07-08 16:55:26 | jharmon-gilead zdz2101 | APPROVED |
Pull Request 119: Fix 118: Standardize activity fields
Merging fix-118-rename_activity_fields into dev
https://github.com/Gilead-Public/gsm.qtl/pull/119
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| jharmon-gilead | 2026-06-01 15:32:18 | zdz2101 lauramaxwell | APPROVED |
Pull Request 117: Fix 116: Add active fields to workflows
Merging fix-116-add_active_fields into dev
https://github.com/Gilead-Public/gsm.qtl/pull/117
| Requester | Date Requested | Reviewers | Review Status |
|---|---|---|---|
| jharmon-gilead | 2026-05-27 14:44:32 | copilot-pull-request-reviewer[bot] zdz2101 | COMMENTED |