Qualification Report for the {gsm} R Package

{gsm} v2.0.1

Report Run Date: 2024-08-14

Introduction

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 R package 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

Test Cases

Test cases translate specifications into testable scripts to confirm that the package functions meet the established requirements. Test cases represent how a user may utilize the function to help identify code gaps and support testing automation.

Test cases for gsm are written using the standard testthat workflow. A single test script is saved for each test case and is named following the convention test_qual_{TestID}.R, where TestID is the test case number. Test code within these scripts is written clearly and concisely to facilitate quick execution and interpretability. Note that a single test case may be associated with multiple specifications.

Test Results: Overview

Function Name	Number of Tests	Number Passed	Number Failed	Number Skipped
Adverse Event Assessment	52	52	0	0
Analysis workflow	22	22	0	0
Analyze_NormalApprox_PredictBounds	19	19	0	0
Data Change Rate Assessment	19	19	0	0
Data Entry Lag Assessment	19	19	0	0
Disposition Assessment	35	35	0	0
Flag_NormalApprox	7	7	0	0
Labs Assessment	19	19	0	0
Mapping workflow	4	3	0	0
Protocol Deviation Assessment	30	30	0	0
Query Age Assessment	35	35	0	0
Query Rate Assessment	35	35	0	0
Summarize	16	16	0	0

Test Results: Detailed

One Row Per Specification

Spec ID	Spec Description	Risk	Impact	Associated Test IDs
S1_1	Given raw participant-level data, all necessary data.frame transformations are made to create input data for all workflows	High	High	T1_1
S2_1	Given raw participant-level data, a properly specified Workflow for a KRI creates summarized and flagged data	High	High	T2_1
S2_2	Given raw participant-level data with missingness, a properly specified Workflow for a KRI creates summarized and flagged data	High	High	T2_2
S3_1	Given pre-processed input data, a properly specified Workflow for a KRI creates summarized and flagged data	High	High	T3_1
S4_1	Given appropriate metadata (i.e. vThresholds), flagged observations are properly marked in summary data	High	High	T4_1
S4_2	Given appropriate metadata (i.e. vThresholds), data.frame of bounds can be created	High	High	T4_2
S5_1	Given appropriate raw participant-level data, flag values can be correctly assigned to records that meet flagging criteria, including custom thresholding.	High	High	T5_1
S5_2	Given appropriate raw participant-level data, flag values are correctly assigned as NA for sites with low enrollment.	High	High	T5_2
S6_1	Given appropriate raw participant-level data, an Adverse Event Assessment can be done using the Normal Approximation method.	High	High	T6_1
S6_2	Adverse Event Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	High	High	T6_2
S7_1	Given appropriate raw participant-level data, a Protocol Deviation Assessment can be done using the Normal Approximation method.	High	High	T7_1
S7_2	Protocol Deviation Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	High	High	T7_2
S8_1	Given appropriate raw participant-level data, a Dispositon Assessment can be done using the Normal Approximation method.	High	High	T8_1
S8_2	Disposition Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	High	High	T8_2
S9_1	Given appropriate raw participant-level data, a Labs Assessment can be done using the Normal Approximation method.	High	High	T9_1
S9_2	Labs Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	High	High	T9_2
S10_1	Given appropriate raw participant-level data, a Data Change Rate Assessment can be done using the Normal Approximation method.	High	High	T10_1
S10_2	Data Change Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	High	High	T10_2
S11_1	Given appropriate raw participant-level data, a Data Entry Lag Assessment can be done using the Normal Approximation method.	High	High	T11_1
S11_2	Data Entry Lag Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	High	High	T11_2
S12_1	Given appropriate raw participant-level data, a Query Age Assessment can be done using the Normal Approximation method.	High	High	T12_1
S12_2	Query Age Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	High	High	T12_2
S13_1	Given appropriate raw participant-level data, a Query Rate Assessment can be done using the Normal Approximation method.	High	High	T13_1
S13_2	Query Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	High	High	T13_2

One Row Per Test

Function	Spec ID	Test ID	Test Description	Test Result
Mapping workflow	S1_1	T1_1	lData is correctly mapped for processing using mapping.yaml in conjunction with MakeWorkflowList() and RunWorkflow	Pass
Analysis workflow	S2_1	T2_1	Given raw participant-level data, a properly specified Workflow for a KRI creates summarized and flagged data	Pass
Analysis workflow	S2_2	T2_2	Given raw participant-level data with missingness, a properly specified Workflow for a KRI creates summarized and flagged data	|Pass
Analysis workflow	S3_1	T3_1	Given pre-processed input data, a properly specified Workflow for a KRI creates summarized and flagged data	Pass
Flag_NormalApprox	S4_1	T4_1	Given appropriate metadata (i.e. vThresholds), flagged observations are properly marked in summary data	Pass
Analyze_NormalApprox_PredictBounds	S4_2	T4_2	Given appropriate metadata (i.e. vThresholds), bounds are properly applied to generate flags	Pass
Summarize	S5_1	T5_1	Given appropriate raw participant-level data, flag values can be correctly assigned to records that meet flagging criteria, including custom thresholding.	Pass
Summarize	S5_2	T5_2	Given appropriate raw participant-level data, flag values are correctly assigned as NA for sites with low enrollment.	Pass
Adverse Event Assessment	S6_1	T6_1	Given appropriate raw participant-level data, an Adverse Event Assessment can be done using the Normal Approximation method.	Pass
Adverse Event Assessment	S6_2	T6_2	Adverse Event Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	Pass
Protocol Deviation Assessment	S7_1	T7_1	Given appropriate raw participant-level data, a Protocol Deviation Assessment can be done using the Normal Approximation method.	Pass
Protocol Deviation Assessment	S7_2	T7_2	Protocol Deviation Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	Pass
Disposition Assessment	S8_1	T8_1	Given appropriate raw participant-level data, a Dispositon Assessment can be done using the Normal Approximation method.	Pass
Disposition Assessment	S8_2	T8_2	Disposition Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	Pass
Labs Assessment	S9_1	T9_1	Given appropriate raw participant-level data, a Labs Assessment can be done using the Normal Approximation method.	Pass
Labs Assessment	S9_2	T9_2	Labs Assessments can be done correctly using a grouping variable, such as Site or Country for KRIs, and Study for QTLs, when applicable.	Pass
Data Change Rate Assessment	S10_1	T10_1	Given appropriate raw participant-level data, a Data Change Rate Assessment can be done using the Normal Approximation method.	Pass
Data Change Rate Assessment	S10_2	T10_2	Data Change Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	Pass
Data Entry Lag Assessment	S11_1	T11_1	Given appropriate raw participant-level data, a Data Entry Lag Assessment can be done using the Normal Approximation method.	Pass
Data Entry Lag Assessment	S11_2	T11_2	Data Entry Lag Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	Pass
Query Age Assessment	S12_1	T12_1	Given appropriate raw participant-level data, a Query Age Assessment can be done using the Normal Approximation method.	Pass
Query Age Assessment	S12_2	T12_2	Query Age Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	Pass
Query Rate Assessment	S13_1	T13_1	Given appropriate raw participant-level data, a Query Rate Assessment can be done using the Normal Approximation method.	Pass
Query Rate Assessment	S13_2	T13_2	Query Rate Assessments can be done correctly using a grouping variable, such as Site, Country, or Study, when applicable.	Pass

Unit Tests

Unit Testing Overview

Unit testing was performed in addition to qualification testing to help ensure that individual pieces of code within the R package function correctly and produce the expected results. By testing individual units of code in isolation, developers can identify and fix issues early in the development process before more significant and scaled problems arise.

Unit Test Coverage

The table below summarizes unit test coverage of each gsm function. This metric quantifies the extent of unit testing. The closer this measure is to 100%, the more unit testing that function has.

Function	File Coverage
R/aaa-shared.R	0.00 %
R/Analyze_Fisher.R	100.00 %
R/Analyze_Identity.R	100.00 %
R/Analyze_NormalApprox_PredictBounds.R	100.00 %
R/Analyze_NormalApprox.R	100.00 %
R/Analyze_Poisson_PredictBounds.R	97.92 %
R/Analyze_Poisson.R	100.00 %
R/Flag_Fisher.R	100.00 %
R/Flag_NormalApprox.R	100.00 %
R/Flag_Poisson.R	100.00 %
R/Flag.R	100.00 %
R/Input_Rate.R	94.92 %
R/Report_FlagOverTime.R	94.68 %
R/Report_FormatFlag.R	100.00 %
R/Report_KRI.R	0.00 %
R/Report_MetricCharts.R	100.00 %
R/Report_MetricTable.R	97.50 %
R/Report_OverviewText.R	100.00 %
R/Report_Setup.R	93.75 %
R/Report_StudyInfo.R	100.00 %
R/Report_Timeline.R	84.92 %
R/RunQuery.R	100.00 %
R/RunStep.R	100.00 %
R/RunWorkflow.R	88.89 %
R/RunWorkflows.R	0.00 %
R/Summarize.R	100.00 %
R/Transform_Count.R	100.00 %
R/Transform_Rate.R	100.00 %
R/util-BindResults.R	100.00 %
R/util-clindata.R	72.73 %
R/util-gt.R	100.00 %
R/util-MakeBounds.R	100.00 %
R/util-MakeCharts.R	100.00 %
R/util-MakeLongMeta.R	100.00 %
R/util-MakeMetric.R	100.00 %
R/util-MakeWideGroups.R	100.00 %
R/util-MakeWorkflowList.R	96.77 %
R/util-ParseThreshold.R	100.00 %
R/util-RenderRmd.R	0.00 %
R/util-Report.R	72.88 %
R/Visualize_Metric.R	94.38 %
R/Visualize_Scatter.R	100.00 %
R/Visualize_Score.R	98.28 %
R/Widget_BarChart.R	76.32 %
R/Widget_FlagOverTime.R	51.61 %
R/Widget_GroupOverview.R	78.95 %
R/Widget_ScatterPlot.R	75.00 %
R/Widget_TimeSeries.R	76.32 %
Total Coverage	90.70 %

Qualification Testing Environment

Session Information

R version 4.4.1 (2024-06-14)

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: RSQLite(v.2.3.7), gsm(v.2.0.1), testthat(v.3.2.1.1), riskmetric(v.0.2.4), stringr(v.1.5.1), gh(v.1.4.1), pander(v.0.6.5), purrr(v.1.0.2), dplyr(v.1.1.4) and knitr(v.1.48)

loaded via a namespace (and not attached): tidyselect(v.1.2.1), viridisLite(v.0.4.2), blob(v.1.2.4), urltools(v.1.7.3), fastmap(v.1.2.0), lazyeval(v.0.2.2), promises(v.1.3.0), rex(v.1.2.1), digest(v.0.6.36), mime(v.0.12), lifecycle(v.1.0.4), waldo(v.0.5.2), ellipsis(v.0.3.2), magrittr(v.2.0.3), compiler(v.4.4.1), rlang(v.1.1.4), sass(v.0.4.9), tools(v.4.4.1), utf8(v.1.2.4), yaml(v.2.3.10), htmlwidgets(v.1.6.4), bit(v.4.0.5), pkgbuild(v.1.4.4), curl(v.5.2.1), here(v.1.0.1), xml2(v.1.3.6), cranlogs(v.2.1.1), pkgload(v.1.4.0), miniUI(v.0.1.1.1), covr(v.3.6.4), withr(v.3.0.1), desc(v.1.4.3), triebeard(v.0.4.1), grid(v.4.4.1), fansi(v.1.0.6), urlchecker(v.1.0.1), profvis(v.0.3.8), xtable(v.1.8-4), colorspace(v.2.1-1), ggplot2(v.3.5.1), scales(v.1.3.0), cli(v.3.6.3), chron(v.2.3-61), rmarkdown(v.2.27), ragg(v.1.3.2), generics(v.0.1.3), remotes(v.2.5.0), rstudioapi(v.0.16.0), httr(v.1.4.7), sessioninfo(v.1.2.2), DBI(v.1.2.3), cachem(v.1.1.0), BiocManager(v.1.30.23), vctrs(v.0.6.5), devtools(v.2.4.5), jsonlite(v.1.8.8), bit64(v.4.0.5), systemfonts(v.1.1.0), tidyr(v.1.3.1), jquerylib(v.0.1.4), proto(v.1.0.0), glue(v.1.7.0), clindata(v.1.0.5), pkgdown(v.2.1.0), stringi(v.1.8.4), gtable(v.0.3.5), later(v.1.3.2), munsell(v.0.5.1), tibble(v.3.2.1), pillar(v.1.9.0), htmltools(v.0.5.8.1), brio(v.1.1.5), R6(v.2.5.1), tcltk(v.4.4.1), textshaping(v.0.4.0), rprojroot(v.2.0.4), kableExtra(v.1.4.0), evaluate(v.0.24.0), shiny(v.1.9.1), highr(v.0.11), gsubfn(v.0.7), backports(v.1.5.0), memoise(v.2.0.1), broom(v.1.0.6), httpuv(v.1.6.15), bslib(v.0.8.0), Rcpp(v.1.0.13), svglite(v.2.1.3), sqldf(v.0.4-11), xfun(v.0.46), fs(v.1.6.4), usethis(v.3.0.0) and pkgconfig(v.2.0.3)

Package List

The table below utilizes the riskmetric package, which quantifies the robustness of an R package. The pkg_score column captures the risk involved with using a package. The risk level ranges from 0 (low risk) to 1 (high risk).

package	version	pkg_score
broom	1.0.6	0.373
cli	3.6.3	0.406
DBI	1.2.3	0.345
dplyr	1.1.4	0.392
fs	1.6.4	0.336
ggplot2	3.5.1	0.404
glue	1.7.0	0.287
htmltools	0.5.8.1	0.404
htmlwidgets	1.6.4	0.316
jsonlite	1.8.8	0.474
magrittr	2.0.3	0.284
purrr	1.0.2	0.369
rlang	1.1.4	0.423
stats	4.4.1	0.704
stringr	1.5.1	0.364
tibble	3.2.1	0.357
tidyr	1.3.1	0.385
tools	4.4.1	0.734
utils	4.4.1	0.687
withr	3.0.1	0.324
yaml	2.3.10	0.429

Pull Request History

Pull Request 1776: Release v2.0.1

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1776

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-12 14:56:50		COMMENTED

Pull Request 1775: update analyticsInput to match with analyticsSummary

Merging fix-1774 into dev

https://github.com/Gilead-BioStats/gsm/pull/1775

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-12 14:04:56	taylorrodgers	APPROVED

Pull Request 1772: Release v2.0.1

Merging release-v2_0_1 into dev

https://github.com/Gilead-BioStats/gsm/pull/1772

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-09 20:05:04	jwildfire

Pull Request 1769: Fix summary tables in reports and add metricTable to Visualize_Metric() output

Merging fix-1765 into dev

https://github.com/Gilead-BioStats/gsm/pull/1769

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-08 17:47:05	jwildfire jonthegeek	APPROVED

Pull Request 1768: fixes #1757 - renders if package is read-only

Merging fix-1767 into dev

https://github.com/Gilead-BioStats/gsm/pull/1768

Requester	Date Requested	Reviewers	Review Status
dpastoor	2024-08-08 17:20:55	lauramaxwell	CHANGES_REQUESTED

Pull Request 1766: Don’t ever use Sys.Date() as SnapshotDate.

Merging fix-1764 into dev

https://github.com/Gilead-BioStats/gsm/pull/1766

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-08 15:37:11		APPROVED

Pull Request 1763: Release v2.0.0

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1763

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-07 17:39:22		APPROVED

Pull Request 1762: Update NEWS.md

Merging news-update into dev

https://github.com/Gilead-BioStats/gsm/pull/1762

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-07 17:15:03		APPROVED

Pull Request 1759: Fix lifecycle badges in headers and reference

Merging fix-1757 into dev

https://github.com/Gilead-BioStats/gsm/pull/1759

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-07 13:39:16		APPROVED

Pull Request 1758: fixup: add dplyr filter namespace

Merging dplyr-namespace into dev

https://github.com/Gilead-BioStats/gsm/pull/1758

Requester	Date Requested	Reviewers	Review Status
dpastoor	2024-08-07 10:22:53		APPROVED

Pull Request 1754: Build sample reports.

Merging fix-1640 into dev

https://github.com/Gilead-BioStats/gsm/pull/1754

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-06 20:56:23		APPROVED

Pull Request 1753: Refactor click callbacks in bar chart, scatter plot, and time series.

Merging fix-1749 into dev

https://github.com/Gilead-BioStats/gsm/pull/1753

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-08-06 20:04:29	taylorrodgers	APPROVED

Pull Request 1751: Fix workflow typo.

Merging fix-1734 into dev

https://github.com/Gilead-BioStats/gsm/pull/1751

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-06 19:22:58		APPROVED

Pull Request 1748: Update qualification_report.yaml to overwrite report if necessary

Merging fix-1747 into dev

https://github.com/Gilead-BioStats/gsm/pull/1748

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-01 14:44:54	jwildfire	APPROVED

Pull Request 1745: some misc code review cleanup/fixups as I go through the RC

Merging devin-misc-tweaks into dev

https://github.com/Gilead-BioStats/gsm/pull/1745

Requester	Date Requested	Reviewers	Review Status
dpastoor	2024-07-31 15:53:05		APPROVED

Pull Request 1741: Simplify R-CMD-check-dev.yaml matrix

Merging fix-1737 into dev

https://github.com/Gilead-BioStats/gsm/pull/1741

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-30 13:16:59	jwildfire	APPROVED

Pull Request 1740: Fix qualification report workflow

Merging fix-1738 into dev

https://github.com/Gilead-BioStats/gsm/pull/1740

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-30 13:16:30		APPROVED

Pull Request 1739: Fix qualification report workflow

Merging gix-1738 into dev

https://github.com/Gilead-BioStats/gsm/pull/1739

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-30 13:13:47

Pull Request 1736: Standardize/clean test-coverage.yaml.

Merging fix-1634 into dev

https://github.com/Gilead-BioStats/gsm/pull/1736

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-30 13:05:11	jwildfire	APPROVED

Pull Request 1732: gsm v2.0.0-RC-1 - Code Review

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1732

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-29 20:34:20

Pull Request 1731: Fix overall group select and group overview sorting.

Merging fix-overall-group-select into dev

https://github.com/Gilead-BioStats/gsm/pull/1731

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-29 20:28:41	jwildfire	APPROVED

Pull Request 1729: Release candidate checklist

Merging fix-1695 into dev

https://github.com/Gilead-BioStats/gsm/pull/1729

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-29 08:17:14	jwildfire	APPROVED

Pull Request 1727: Odds and Ends for v2.0 release

Merging fix-1707 into dev

https://github.com/Gilead-BioStats/gsm/pull/1727

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-26 10:54:12		CHANGES_REQUESTED

Pull Request 1719: refactor widget controls

Merging fix-widgets into dev

https://github.com/Gilead-BioStats/gsm/pull/1719

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-25 21:03:32	jwildfire taylorrodgers	CHANGES_REQUESTED

Pull Request 1718: Fix pkgdown

Merging fix-1706 into dev

https://github.com/Gilead-BioStats/gsm/pull/1718

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-25 20:16:16		APPROVED

Pull Request 1716: update data model vignette

Merging DataModelVignette into dev

https://github.com/Gilead-BioStats/gsm/pull/1716

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-25 12:59:48		APPROVED

Pull Request 1715: Remove all QTL functions, tests and docs

Merging fix-1712 into dev

https://github.com/Gilead-BioStats/gsm/pull/1715

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-25 07:07:45		CHANGES_REQUESTED

Pull Request 1714: Format flags properly with Report_FormatFlag.

Merging fix-1713 into dev

https://github.com/Gilead-BioStats/gsm/pull/1714

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-24 20:16:42	jwildfire	APPROVED

Pull Request 1709: Added gsm article links to ReadMe

Merging fix-1566 into dev

https://github.com/Gilead-BioStats/gsm/pull/1709

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-24 14:59:45		APPROVED

Pull Request 1708: remove /man/md folder

Merging fix-1701 into dev

https://github.com/Gilead-BioStats/gsm/pull/1708

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-24 12:54:05		APPROVED

Pull Request 1705: KRI Over Time Demo App

Merging overTimeAppsPOC into dev

https://github.com/Gilead-BioStats/gsm/pull/1705

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-23 19:26:49	jwildfire	APPROVED

Pull Request 1702: Update headers with glossary and simplified examples

Merging fix-1628 into dev

https://github.com/Gilead-BioStats/gsm/pull/1702

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-23 15:14:18		CHANGES_REQUESTED

Pull Request 1700: Run styler on R/ and tests/

Merging fix-1698 into dev

https://github.com/Gilead-BioStats/gsm/pull/1700

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-23 13:24:27		APPROVED

Pull Request 1697: Replace strThreshold with Threshold

Merging fix-1674 into dev

https://github.com/Gilead-BioStats/gsm/pull/1697

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-23 11:52:03	jonthegeek	APPROVED

Pull Request 1696: Add Data Reporting Vignette

Merging fix-1613 into dev

https://github.com/Gilead-BioStats/gsm/pull/1696

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-23 11:03:57		APPROVED

Pull Request 1690: Test workflows

Merging fix-1680 into dev

https://github.com/Gilead-BioStats/gsm/pull/1690

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-19 16:39:28	jwildfire	APPROVED

Pull Request 1687: update MakeBounds() to allow Poisson bounds to be created

Merging fix-1684 into dev

https://github.com/Gilead-BioStats/gsm/pull/1687

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-19 13:35:33	jwildfire	APPROVED

Pull Request 1683: Faster RunWorkflow() tests

Merging fix-1635 into dev

https://github.com/Gilead-BioStats/gsm/pull/1683

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-18 21:04:29	jwildfire	APPROVED

Pull Request 1679: Update examples

Merging update-examples into dev

https://github.com/Gilead-BioStats/gsm/pull/1679

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-18 15:40:17	jonthegeek	APPROVED

Pull Request 1677: Update Cookbook.Rmd to reference inst/examples

Merging fix-1668 into dev

https://github.com/Gilead-BioStats/gsm/pull/1677

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-18 07:51:56	jwildfire	COMMENTED

Pull Request 1676: Vignette Updates

Merging fix-1649 into dev

https://github.com/Gilead-BioStats/gsm/pull/1676

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-18 07:27:37		CHANGES_REQUESTED

Pull Request 1675: Move dfBounds to Reporting model

Merging fix-1670 into dev

https://github.com/Gilead-BioStats/gsm/pull/1675

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-17 20:09:22		APPROVED

Pull Request 1672: Add util tests

Merging fix-1669 into dev

https://github.com/Gilead-BioStats/gsm/pull/1672

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-17 15:24:41	jwildfire	APPROVED

Pull Request 1667: Implement a glossary

Merging fix-1658 into dev

https://github.com/Gilead-BioStats/gsm/pull/1667

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-16 20:11:23		COMMENTED

Pull Request 1666: Update all sampleData to use analyticsX and reportingX

Merging fix-1662 into dev

https://github.com/Gilead-BioStats/gsm/pull/1666

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-16 15:56:47	jwildfire	APPROVED

Pull Request 1665: Incorporate FlagOverTime to standard report

Merging fix-1653 into dev

https://github.com/Gilead-BioStats/gsm/pull/1665

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-16 15:22:24

Pull Request 1663: Fix overall group select in Report_KRI .

Merging fix-1654 into dev

https://github.com/Gilead-BioStats/gsm/pull/1663

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-16 14:50:23	jwildfire	APPROVED

Pull Request 1661: Fix sampleData

Merging fix-1651 into dev

https://github.com/Gilead-BioStats/gsm/pull/1661

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-16 08:24:34		APPROVED

Pull Request 1657: Standardize gt usage

Merging fix-1652 into dev

https://github.com/Gilead-BioStats/gsm/pull/1657

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-15 17:04:06	jwildfire	CHANGES_REQUESTED

Pull Request 1656: fix #1616

Merging fix-1616 into dev

https://github.com/Gilead-BioStats/gsm/pull/1656

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-15 16:58:46	jwildfire	APPROVED

Pull Request 1650: tweaks

Merging fix-group-overview-css into fix-report

https://github.com/Gilead-BioStats/gsm/pull/1650

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-12 20:23:10		APPROVED

Pull Request 1648: Remove Legacy Datasets

Merging fix-1642 into dev

https://github.com/Gilead-BioStats/gsm/pull/1648

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-11 22:32:41		APPROVED

Pull Request 1647: Add strGroupLevel to Input_Rate and update workflows

Merging fix-1646 into fix-report-rbmViz

https://github.com/Gilead-BioStats/gsm/pull/1647

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-11 21:55:58		APPROVED

Pull Request 1645: Integrate {gsm} and rbmViz .

Merging fix-report-rbmViz into fix-report

https://github.com/Gilead-BioStats/gsm/pull/1645

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-11 20:36:09	lauramaxwell	APPROVED

Pull Request 1639: add example for creating a new missing visit KRI

Merging fix-1488 into dev

https://github.com/Gilead-BioStats/gsm/pull/1639

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-11 12:31:53		APPROVED

Pull Request 1638: Fix 1606

Merging fix-1606 into dev

https://github.com/Gilead-BioStats/gsm/pull/1638

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-10 21:36:54		APPROVED

Pull Request 1632: Fix 1631

Merging fix-1631 into dev

https://github.com/Gilead-BioStats/gsm/pull/1632

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-09 18:03:44	jwildfire	COMMENTED

Pull Request 1630: Group > GroupLevel

Merging fix-report-GroupLevel into fix-report

https://github.com/Gilead-BioStats/gsm/pull/1630

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-07-09 13:53:55	lauramaxwell

Pull Request 1629: Add sample reporting data

Merging fix-1626 into dev

https://github.com/Gilead-BioStats/gsm/pull/1629

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-08 20:51:59		COMMENTED

Pull Request 1627: KRI Report generation

Merging fix-report into dev

https://github.com/Gilead-BioStats/gsm/pull/1627

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-08 16:42:16		APPROVED

Pull Request 1625: Update Data Pipeline vignette

Merging fix-1580 into dev

https://github.com/Gilead-BioStats/gsm/pull/1625

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-05 18:41:30	jwildfire	CHANGES_REQUESTED

Pull Request 1621: Fix tests, examples and documentation for checks

Merging fix-1620 into dev

https://github.com/Gilead-BioStats/gsm/pull/1621

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-07-05 12:39:29	andersonjake1988	APPROVED

Pull Request 1619: Add country dropdown to scatterplot

Merging fix-1543 into dev

https://github.com/Gilead-BioStats/gsm/pull/1619

Requester	Date Requested	Reviewers	Review Status
taylorrodgers	2024-07-02 13:43:12	lauramaxwell	CHANGES_REQUESTED

Pull Request 1618: Update Widget_SiteOverview tests.

Merging fix-1617 into dev

https://github.com/Gilead-BioStats/gsm/pull/1618

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-07-01 19:42:56		APPROVED

Pull Request 1615: v2 Qualification Test Updates

Merging fix-1533 into dev

https://github.com/Gilead-BioStats/gsm/pull/1615

Requester	Date Requested	Reviewers	Review Status
andersonjake1988	2024-06-28 16:33:23		CHANGES_REQUESTED

Pull Request 1614: Workflow Improvements

Merging fix-1592 into dev

https://github.com/Gilead-BioStats/gsm/pull/1614

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-06-28 15:03:36	samussiah	APPROVED

Pull Request 1612: Update Input_Rate output

Merging fix-1608 into dev

https://github.com/Gilead-BioStats/gsm/pull/1612

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-27 20:48:57	jwildfire	APPROVED

Pull Request 1610: Update tests for analysis workflow functions

Merging fix-1551 into dev

https://github.com/Gilead-BioStats/gsm/pull/1610

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-27 20:43:13	jwildfire	COMMENTED

Pull Request 1609: Fix thresholds.

Merging fix-1596 into fix-1592

https://github.com/Gilead-BioStats/gsm/pull/1609

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-06-27 13:44:47	lauramaxwell jwildfire	APPROVED

Pull Request 1605: Add Reporting Workflow

Merging fix-1597 into dev

https://github.com/Gilead-BioStats/gsm/pull/1605

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-06-26 15:27:11	samussiah	APPROVED

Pull Request 1603: Update Data Analysis vignette

Merging fix-1581 into dev

https://github.com/Gilead-BioStats/gsm/pull/1603

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-26 14:40:21		CHANGES_REQUESTED

Pull Request 1600: Fix 1593

Merging fix-1593 into dev

https://github.com/Gilead-BioStats/gsm/pull/1600

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-06-25 21:31:14	samussiah lauramaxwell

Pull Request 1598: Clean up inst folder

Merging fix-1591 into dev

https://github.com/Gilead-BioStats/gsm/pull/1598

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-25 12:26:09		APPROVED

Pull Request 1594: Site overview table

Merging fix-1457 into dev

https://github.com/Gilead-BioStats/gsm/pull/1594

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-06-24 17:12:14	lauramaxwell	APPROVED

Pull Request 1589: Fix 1587

Merging fix-1587 into dev

https://github.com/Gilead-BioStats/gsm/pull/1589

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-06-21 14:26:55

Pull Request 1588: Add demo scripts

Merging fix-1587 into dev

https://github.com/Gilead-BioStats/gsm/pull/1588

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-20 21:19:01		APPROVED

Pull Request 1586: Cookbook vignette update

Merging fix-1579 into dev

https://github.com/Gilead-BioStats/gsm/pull/1586

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-20 18:39:22		APPROVED

Pull Request 1584: Update README.md with correct KRI metric names

Merging fix-1557 into dev

https://github.com/Gilead-BioStats/gsm/pull/1584

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-17 19:55:22		APPROVED

Pull Request 1582: augmented RunWorkflow and fixed tests

Merging fix-1577 into dev

https://github.com/Gilead-BioStats/gsm/pull/1582

Requester	Date Requested	Reviewers	Review Status
andersonjake1988	2024-06-13 21:21:24		COMMENTED

Pull Request 1578: Update naming conventions in workflow helper function and fix pkgdown reporting step

Merging fix-1554 into dev

https://github.com/Gilead-BioStats/gsm/pull/1578

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-13 13:29:13		APPROVED

Pull Request 1574: Add nMinDenominator param to yaml workflows and update all column names of dfs fed into widgets

Merging fix-1568 into dev

https://github.com/Gilead-BioStats/gsm/pull/1574

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-11 14:28:17		APPROVED

Pull Request 1572: Create sampleInput data and update tests and headers to use it

Merging fix-1550 into dev

https://github.com/Gilead-BioStats/gsm/pull/1572

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-06-10 14:42:20		APPROVED

Pull Request 1570: Flags over time table

Merging FlagOverTime into fix-report

https://github.com/Gilead-BioStats/gsm/pull/1570

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-06-08 11:40:57

Pull Request 1565: change GroupType to GroupLevel

Merging fix-1564 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1565

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-05-31 17:54:52		APPROVED

Pull Request 1563: Mark all QTL functions as experimental

Merging fix-1553 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1563

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-05-31 15:10:57		APPROVED

Pull Request 1555: add counts workflow

Merging fix-1544 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1555

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-05-28 14:56:12		APPROVED

Pull Request 1549: QC: Add tests for new v2 files

Merging fix-1539 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1549

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-05-23 15:14:56		COMMENTED

Pull Request 1548: fix: KRI reporting bugs

Merging fix-1547 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1548

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-05-21 17:09:33		APPROVED

Pull Request 1546: add vThreshold in meta. fix #1542

Merging fix-1542 into fix-1538

https://github.com/Gilead-BioStats/gsm/pull/1546

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-05-14 15:59:10		APPROVED

Pull Request 1545: Data Pipeline Standardization

Merging fix-1538 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1545

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-05-14 03:17:34		COMMENTED

Pull Request 1537: Fix 1530 and fix 1531

Merging fix-1530-and-fix-1531 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1537

Requester	Date Requested	Reviewers	Review Status
taylorrodgers	2024-05-02 18:07:26		CHANGES_REQUESTED

Pull Request 1534: Remove/Update existing unit tests

Merging fix-1532 into v2-dev

https://github.com/Gilead-BioStats/gsm/pull/1534

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-05-01 20:44:39		APPROVED

Pull Request 1528: v1.9.3 Release

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1528

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-04-24 16:32:59

Pull Request 1525: V2 dev

Merging v2-dev into dev

https://github.com/Gilead-BioStats/gsm/pull/1525

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-04-24 09:47:17	dpastoor	APPROVED

Pull Request 1524: add site overview table widget

Merging site-overview-table into dev

https://github.com/Gilead-BioStats/gsm/pull/1524

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-04-23 18:40:03	jwildfire

Pull Request 1521: Remove references to unused columns in mapping functions and specs.

Merging fix-1520 into dev

https://github.com/Gilead-BioStats/gsm/pull/1521

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-04-08 23:57:44	jwildfire	APPROVED

Pull Request 1518: Add site metadata to each chart module.

Merging add-site-metadata into dev

https://github.com/Gilead-BioStats/gsm/pull/1518

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-04-04 21:59:50	andersonjake1988	APPROVED

Pull Request 1517: Extend Run_Workflow functionality

Merging wf-proto into dev

https://github.com/Gilead-BioStats/gsm/pull/1517

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-04-04 20:32:55	dpastoor samussiah

Pull Request 1513: Fix 1512

Merging fix-1512 into dev

https://github.com/Gilead-BioStats/gsm/pull/1513

Requester	Date Requested	Reviewers	Review Status
mattroumaya	2024-03-29 20:55:22