Qualification Report for the {gsm} R Package

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
Adverse Event Assessment	52	52
Analysis workflow	22	22
Analyze_NormalApprox_PredictBounds	19	19
Data Change Rate Assessment	19	19
Data Entry Lag Assessment	19	19
Disposition Assessment	35	35
Flag_NormalApprox	7	7
Labs Assessment	19	19
Mapping workflow	46	46
Protocol Deviation Assessment	30	30
Query Age Assessment	35	35
Query Rate Assessment	35	35
Summarize	16	16

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	mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected	Pass
Mapping workflow	S1_1	T1_1	mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected	Pass
Mapping workflow	S1_1	T1_1	mappings now done by individual domain, test that inputs and outputs of priority 3 mappings are completed as expected	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/data-specs.R	0.00 %
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	91.80 %
R/Report_FlagOverTime.R	100.00 %
R/Report_FormatFlag.R	100.00 %
R/Report_KRI.R	0.00 %
R/Report_MetricCharts.R	97.78 %
R/Report_MetricTable.R	100.00 %
R/Report_OverviewText.R	100.00 %
R/Report_Setup.R	91.89 %
R/Report_StudyInfo.R	100.00 %
R/Report_Timeline.R	84.92 %
R/RunQuery.R	100.00 %
R/RunStep.R	87.50 %
R/RunWorkflow.R	86.05 %
R/RunWorkflows.R	100.00 %
R/Summarize.R	100.00 %
R/Transform_Count.R	100.00 %
R/Transform_Rate.R	100.00 %
R/util-ApplySpec.R	69.57 %
R/util-BindResults.R	100.00 %
R/util-CalculatePercentage.R	61.54 %
R/util-checkSpec.R	100.00 %
R/util-clindata.R	72.73 %
R/util-CombineSpecs.R	96.43 %
R/util-gt.R	75.00 %
R/util-Ingest.R	95.65 %
R/util-MakeBounds.R	84.78 %
R/util-MakeCharts.R	100.00 %
R/util-MakeLongMeta.R	100.00 %
R/util-MakeMetric.R	84.62 %
R/util-MakeMetricTable.R	100.00 %
R/util-MakeParamLabels.R	100.00 %
R/util-MakeStudyInfo.R	100.00 %
R/util-MakeWideGroups.R	100.00 %
R/util-MakeWorkflowList.R	90.16 %
R/util-ParseThreshold.R	100.00 %
R/util-RenderRmd.R	0.00 %
R/util-Report.R	81.71 %
R/Visualize_Metric.R	94.34 %
R/Visualize_Scatter.R	100.00 %
R/Visualize_Score.R	100.00 %
R/Widget_BarChart.R	81.25 %
R/Widget_FlagOverTime.R	71.15 %
R/Widget_GroupOverview.R	82.22 %
R/Widget_ScatterPlot.R	80.95 %
R/Widget_TimeSeries.R	81.25 %
Total Coverage	90.75 %

Qualification Testing Environment

Session Information

R version 4.4.2 (2024-10-31)

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: tcltk, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: RSQLite(v.2.3.7), gsm(v.2.1.2), 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), knitr(v.1.49) and gt(v.0.11.1)

loaded via a namespace (and not attached): tidyselect(v.1.2.1), 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.0.6.37), mime(v.0.12), lifecycle(v.1.0.4), waldo(v.0.6.1), ellipsis(v.0.3.2), magrittr(v.2.0.3), compiler(v.4.4.2), rlang(v.1.1.4), sass(v.0.4.9), tools(v.4.4.2), utf8(v.1.2.4), yaml(v.2.3.10), htmlwidgets(v.1.6.4), bit(v.4.5.0), pkgbuild(v.1.4.5), curl(v.6.0.0), 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.3.0.2), desc(v.1.4.3), triebeard(v.0.4.1), grid(v.4.4.2), fansi(v.1.0.6), urlchecker(v.1.0.1), profvis(v.0.4.0), 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.2.29), ragg(v.1.3.3), generics(v.0.1.3), remotes(v.2.5.0), rstudioapi(v.0.17.1), httr(v.1.4.7), sessioninfo(v.1.2.2), DBI(v.1.2.3), cachem(v.1.1.0), BiocManager(v.1.30.25), vctrs(v.0.6.5), devtools(v.2.4.5), jsonlite(v.1.8.9), bit64(v.4.5.2), systemfonts(v.1.1.0), tidyr(v.1.3.1), jquerylib(v.0.1.4), proto(v.1.0.0), glue(v.1.8.0), clindata(v.1.0.5), pkgdown(v.2.1.1), stringi(v.1.8.4), gtable(v.0.3.6), 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), textshaping(v.0.4.0), rprojroot(v.2.0.4), evaluate(v.1.0.1), shiny(v.1.9.1), gsubfn(v.0.7), backports(v.1.5.0), memoise(v.2.0.1), broom(v.1.0.7), httpuv(v.1.6.15), bslib(v.0.8.0), Rcpp(v.1.0.13-1), sqldf(v.0.4-11), xfun(v.0.49), fs(v.1.6.5), 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	1.0.7	0.319
cli	3.6.3	0.394
dplyr	1.1.4	0.394
ggplot2	3.5.1	0.395
glue	1.8.0	0.276
gt	0.11.1	0.444
htmltools	0.5.8.1	0.409
htmlwidgets	1.6.4	0.318
jsonlite	1.8.9	0.472
lifecycle	1.0.4	0.314
magrittr	2.0.3	0.288
methods	4.4.2	0.785
purrr	1.0.2	0.367
rlang	1.1.4	0.420
stats	4.4.2	0.704
stringr	1.5.1	0.349
tibble	3.2.1	0.353
tidyr	1.3.1	0.359
tools	4.4.2	0.734
utils	4.4.2	0.687
yaml	2.3.10	0.429

Pull Request History

Pull Request 1947: Release v2.1.2

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1947

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-11-14 17:21:03	zdz2101	APPROVED

Pull Request 1945: PD > IPD and display site activation / participant enrollment in study info.

Merging fix-1918 into gsm-v2.1.2-rc

https://github.com/Gilead-BioStats/gsm/pull/1945

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-11-14 15:03:08	jwildfire	COMMENTED

Pull Request 1942: gsm v2.1.2 release candidate

Merging gsm-v2.1.2-rc into dev

https://github.com/Gilead-BioStats/gsm/pull/1942

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-11-12 18:16:17	samussiah	APPROVED

Pull Request 1941: Add act_fpfv and est_fpfv to STUDY.yaml spec

Merging fix-1940 into dev

https://github.com/Gilead-BioStats/gsm/pull/1941

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-11-12 14:16:17		APPROVED

Pull Request 1932: Closes #1928 swaps out last remnants of `kable` and `kableExtra` in favor of `gt`

Merging fix-1928 into dev

https://github.com/Gilead-BioStats/gsm/pull/1932

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-11-06 20:18:22	jonthegeek	COMMENTED

Pull Request 1931: Closes #1882 adds a toggle to display past year or full data

Merging fix-1882 into dev

https://github.com/Gilead-BioStats/gsm/pull/1931

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-11-05 18:41:05	jonthegeek	COMMENTED

Pull Request 1930: Update `Metrics.yaml` to not generate `lWorkflows` within steps

Merging fix-1929 into dev

https://github.com/Gilead-BioStats/gsm/pull/1930

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-11-04 21:09:11	jwildfire	COMMENTED

Pull Request 1926: Fix country metadata

Merging fix-country-metadata into dev

https://github.com/Gilead-BioStats/gsm/pull/1926

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-11-04 15:05:39	zdz2101	APPROVED

Pull Request 1923: Fix Ingest return value

Merging Ingest-docs-typo into dev

https://github.com/Gilead-BioStats/gsm/pull/1923

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-30 13:47:28	lauramaxwell	APPROVED

Pull Request 1917: Keep bg color for switch.

Merging fix-1916 into dev

https://github.com/Gilead-BioStats/gsm/pull/1917

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-28 15:42:51		APPROVED

Pull Request 1915: Add Nickname to report header and fix `RunQuery` bug

Merging fix-1878 into dev

https://github.com/Gilead-BioStats/gsm/pull/1915

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-28 14:32:07	andersonjake1988	APPROVED

Pull Request 1913: updated class structure

Merging fix-1912 into dev

https://github.com/Gilead-BioStats/gsm/pull/1913

Requester	Date Requested	Reviewers	Review Status
andersonjake1988	2024-10-25 16:34:05		APPROVED

Pull Request 1910: avoid column name conflicts between `Groups` and `Results`

Merging lock-down-groups into dev

https://github.com/Gilead-BioStats/gsm/pull/1910

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-10-24 18:00:51		APPROVED

Pull Request 1909: Release v2.1.1

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1909

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-23 21:25:59		APPROVED

Pull Request 1908: Fix country overview text

Merging fix-country-overview-text into dev

https://github.com/Gilead-BioStats/gsm/pull/1908

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-23 20:33:45		APPROVED

Pull Request 1907: Update rbm-viz.

Merging rbm-viz-2.1.0 into dev

https://github.com/Gilead-BioStats/gsm/pull/1907

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-23 18:47:10		APPROVED

Pull Request 1906: Embed necessary dependencies in Report_StudyInfo().

Merging fix-1905 into dev

https://github.com/Gilead-BioStats/gsm/pull/1906

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-23 17:15:14		APPROVED

Pull Request 1904: Gsm v2.1.1 release candidate

Merging gsm-v2.1.1-rc into dev

https://github.com/Gilead-BioStats/gsm/pull/1904

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-21 20:20:24	zdz2101 jwildfire	APPROVED

Pull Request 1903: Fix overall group select bug.

Merging fix-1902 into dev

https://github.com/Gilead-BioStats/gsm/pull/1903

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-10-18 20:34:37	zdz2101	APPROVED

Pull Request 1901: Closes #1890 and #1900 to properly check for dates and fix other bugs in checkSpec

Merging fix-1890 into dev

https://github.com/Gilead-BioStats/gsm/pull/1901

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-18 18:10:48	zdz2101	COMMENTED

Pull Request 1899: Closes #1880 add site/participant target numbers and labels to `STUDY.yaml`

Merging fix-1880 into dev

https://github.com/Gilead-BioStats/gsm/pull/1899

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-17 21:01:47		COMMENTED

Pull Request 1898: Flag colors

Merging fix-1896 into dev

https://github.com/Gilead-BioStats/gsm/pull/1898

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-17 15:48:50		APPROVED

Pull Request 1897: Closes #1894 address bug in `Input_Rate()` for 0 row dataframe inputs for dfNumerator/dfDenominator

Merging fix-1894 into dev

https://github.com/Gilead-BioStats/gsm/pull/1897

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-17 15:46:12		APPROVED

Pull Request 1892: Closes #1877 and #1883 addressing bugfixes related to `StudyID` on `Report_Setup()` and `reportingXXXX` datasets

Merging fix-1877 into dev

https://github.com/Gilead-BioStats/gsm/pull/1892

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-15 21:01:24	samussiah	COMMENTED

Pull Request 1891: Only show flag-rows in Report_FlagOverTime()

Merging fix-1879 into dev

https://github.com/Gilead-BioStats/gsm/pull/1891

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-15 15:50:40

Pull Request 1889: Resolve errors related to missing data and an incomplete set of `MetricID` in `dfBounds` .

Merging missing-data-fixes into dev

https://github.com/Gilead-BioStats/gsm/pull/1889

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-10-14 22:25:59	zdz2101 lauramaxwell	APPROVED

Pull Request 1885: Make Report_StudyInfo() Friendlier to Shiny

Merging fix-1799 into dev

https://github.com/Gilead-BioStats/gsm/pull/1885

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-10-14 18:12:12		APPROVED

Pull Request 1884: Closes #1659 and #1660 to use `gt()` instead of `kbl()` in our functions and reports

Merging fix-1660 into dev

https://github.com/Gilead-BioStats/gsm/pull/1884

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-14 16:17:13	lauramaxwell samussiah	CHANGES_REQUESTED

Pull Request 1876: Fix country report

Merging fix-country-report into dev

https://github.com/Gilead-BioStats/gsm/pull/1876

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-10-10 18:31:08	lauramaxwell	APPROVED

Pull Request 1875: Closes #1872 fix miscellaneous aesthetics things and issues

Merging fix-1872 into dev

https://github.com/Gilead-BioStats/gsm/pull/1875

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-10 18:24:25		COMMENTED

Pull Request 1871: yes to true in yamls

Merging yaml-fix-2.1 into dev

https://github.com/Gilead-BioStats/gsm/pull/1871

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-08 19:06:56		APPROVED

Pull Request 1870: Release v2.1.0

Merging dev into main

https://github.com/Gilead-BioStats/gsm/pull/1870

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-08 18:29:43		COMMENTED

Pull Request 1869: Closes #1863 address small bugs in `MakeWorkflowList()` run as intended

Merging fix-1863 into dev

https://github.com/Gilead-BioStats/gsm/pull/1869

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-10-07 17:30:17	jwildfire	COMMENTED

Pull Request 1867: Gsm v2.1.0 Release Candidate

Merging gsm-v2.1.0-rc into dev

https://github.com/Gilead-BioStats/gsm/pull/1867

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-10-04 14:31:53	jwildfire	APPROVED

Pull Request 1865: Workflow updates.

Merging gsm.template-updates into dev

https://github.com/Gilead-BioStats/gsm/pull/1865

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-10-01 15:01:35	lauramaxwell

Pull Request 1864: Load/Save - Take 2

Merging template-refactor-take2 into dev

https://github.com/Gilead-BioStats/gsm/pull/1864

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-09-30 21:36:28		COMMENTED

Pull Request 1862: Closes #1859 checks and updates qualification tests in test/testqualification to align with new workflows for v2.1.0 release

Merging fix-1859 into dev

https://github.com/Gilead-BioStats/gsm/pull/1862

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-26 19:51:16	andersonjake1988	COMMENTED

Pull Request 1861: Run `{gsm}` using local data store.

Merging gsm.template-updates into dev

https://github.com/Gilead-BioStats/gsm/pull/1861

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-09-25 17:43:50	jwildfire	COMMENTED

Pull Request 1856: Add `rbm-viz` v2.1.0.

Merging fix-1855 into dev

https://github.com/Gilead-BioStats/gsm/pull/1856

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-09-24 13:11:22		APPROVED

Pull Request 1853: Discuss #1848 sections of package where there’s a difference of usage between `gt` vs “not”- `gt`

Merging fix-1848 into dev

https://github.com/Gilead-BioStats/gsm/pull/1853

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-19 20:18:58		COMMENTED

Pull Request 1852: Ingest modular

Merging ingest-modular into ingest

https://github.com/Gilead-BioStats/gsm/pull/1852

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-09-19 16:31:37	samussiah	COMMENTED

Pull Request 1851: Update `checkSpec()` cli message to handle `_all` required

Merging fix-1845 into dev

https://github.com/Gilead-BioStats/gsm/pull/1851

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-19 13:31:01	jwildfire samussiah	APPROVED

Merging fix-1653-v0.2.1 into dev

https://github.com/Gilead-BioStats/gsm/pull/1850

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-18 17:53:55	jwildfire	COMMENTED

Pull Request 1849: MakeStudyInfo() function

Merging fix-1820 into dev

https://github.com/Gilead-BioStats/gsm/pull/1849

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-09-17 20:31:37		APPROVED

Pull Request 1847: make analysis workflow work

Merging workflow-tweaks into ingest

https://github.com/Gilead-BioStats/gsm/pull/1847

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-09-17 15:14:12	jonthegeek lauramaxwell	APPROVED

Pull Request 1844: Add `subjid` to EDC domains in mapping workflow.

Merging fix-1761 into ingest

https://github.com/Gilead-BioStats/gsm/pull/1844

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-09-13 16:53:31	lauramaxwell	APPROVED

Pull Request 1843: MakeMetricTable()

Merging fix-1835 into dev

https://github.com/Gilead-BioStats/gsm/pull/1843

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-09-13 16:11:28		COMMENTED

Pull Request 1841: Refactor Data Ingestion Workflow

Merging ingest into dev

https://github.com/Gilead-BioStats/gsm/pull/1841

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-09-13 09:16:58	samussiah	COMMENTED

Pull Request 1839: skip `Analysis_` checks in checkSpec

Merging fix-1837 into dev

https://github.com/Gilead-BioStats/gsm/pull/1839

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-12 21:56:47

Pull Request 1833: Closes #1636 allows `Visualize_Metric()` to run on just results

Merging fix-1636 into dev

https://github.com/Gilead-BioStats/gsm/pull/1833

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-11 22:39:35		COMMENTED

Merging fix-1728 into dev

https://github.com/Gilead-BioStats/gsm/pull/1831

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-10 17:54:23		COMMENTED

Merging fix-1795 into dev

https://github.com/Gilead-BioStats/gsm/pull/1829

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-09 19:18:56		COMMENTED

Pull Request 1828: Update sample reporting data

Merging fix-1800 into dev

https://github.com/Gilead-BioStats/gsm/pull/1828

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-09 17:48:52		APPROVED

Pull Request 1827: Add all required spec tables to workflows

Merging fix-1819 into dev

https://github.com/Gilead-BioStats/gsm/pull/1827

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-06 16:00:38	jwildfire	CHANGES_REQUESTED

Pull Request 1826: Update PR template

Merging fix-1825 into dev

https://github.com/Gilead-BioStats/gsm/pull/1826

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-05 20:51:10		APPROVED

Pull Request 1824: Closes #1686 Renders a message in `KRI_Report()` when there are 0 rows in the summary table

Merging fix-1686 into dev

https://github.com/Gilead-BioStats/gsm/pull/1824

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-05 20:30:12		COMMENTED

Pull Request 1817: Cloes #1678 standardize use of `cli_inform()` and `cli_warn()`

Merging fix-1678 into dev

https://github.com/Gilead-BioStats/gsm/pull/1817

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-05 16:09:46	jonthegeek	COMMENTED

Pull Request 1815: Closes #1779 Enhance `CombineSpecs()` with deduplication, enforcing `required` and adding checks for `type`

Merging fix-1779 into dev

https://github.com/Gilead-BioStats/gsm/pull/1815

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-04 19:36:26	jonthegeek	APPROVED

Pull Request 1814: Add type validation to `CheckSpec()`

Merging fix-1810 into dev

https://github.com/Gilead-BioStats/gsm/pull/1814

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-04 15:44:14		APPROVED

Pull Request 1813: gsm extensions vignette

Merging fix-1805 into dev

https://github.com/Gilead-BioStats/gsm/pull/1813

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-04 14:29:35		COMMENTED

Pull Request 1812: Closes #1722 Study Status Table display bugfix of indiscriminant first five attributes

Merging fix-1722 into dev

https://github.com/Gilead-BioStats/gsm/pull/1812

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-03 19:26:49		COMMENTED

Merging fix-1760 into dev

https://github.com/Gilead-BioStats/gsm/pull/1811

Requester	Date Requested	Reviewers	Review Status
zdz2101	2024-09-03 16:51:27		APPROVED

Pull Request 1809: Simpler depends

Merging withr-depends into dev

https://github.com/Gilead-BioStats/gsm/pull/1809

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-09-03 16:37:13		APPROVED

Pull Request 1808: Add `type` field and query columns to all `spec` s

Merging fix-1778 into dev

https://github.com/Gilead-BioStats/gsm/pull/1808

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-09-03 13:11:23	jwildfire dpastoor	APPROVED

Pull Request 1803: Report_StudyInfo: Show/Hide

Merging fix-1802 into dev

https://github.com/Gilead-BioStats/gsm/pull/1803

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-28 13:23:51		APPROVED

Pull Request 1798: Implement filter args in Input_Rate.

Merging fix-1784 into dev

https://github.com/Gilead-BioStats/gsm/pull/1798

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-22 17:47:16	jwildfire

Pull Request 1791: Add a function to cleanly convert Params to Labels.

Merging fix-1790 into dev

https://github.com/Gilead-BioStats/gsm/pull/1791

Requester	Date Requested	Reviewers	Review Status
jonthegeek	2024-08-19 21:34:15	jwildfire	CHANGES_REQUESTED

Pull Request 1789: Add explicit snapshot date subset to `Widget_GroupOverview` .

Merging fix-1787 into dev

https://github.com/Gilead-BioStats/gsm/pull/1789

Requester	Date Requested	Reviewers	Review Status
samussiah	2024-08-19 17:56:30	jwildfire	CHANGES_REQUESTED

Pull Request 1786: Use `required` param from `spec` in `CheckSpec()`

Merging fix-1777 into reporting-workflow

https://github.com/Gilead-BioStats/gsm/pull/1786

Requester	Date Requested	Reviewers	Review Status
lauramaxwell	2024-08-19 13:54:18		APPROVED

Pull Request 1785: Mapping workflow refactor

Merging mapping-refactor into reporting-workflow

https://github.com/Gilead-BioStats/gsm/pull/1785

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-08-15 15:33:12	dpastoor	COMMENTED

Pull Request 1783: Reporting Workflow Refactor

Merging reporting-workflow into dev

https://github.com/Gilead-BioStats/gsm/pull/1783

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-08-15 14:31:16	samussiah	COMMENTED

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 1746: Prototype Data Specification Framework

Merging mapping-demo into dev

https://github.com/Gilead-BioStats/gsm/pull/1746

Requester	Date Requested	Reviewers	Review Status
jwildfire	2024-07-31 18:04:00	jonthegeek	COMMENTED

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

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

{gsm} v2.1.2

Report Run Date: 2024-11-14

Introduction

Scope

Process Overview

Specifications

Test Cases

Test Results: Overview

Test Results: Detailed

One Row Per Specification

One Row Per Test

Unit Tests

Unit Testing Overview

Unit Test Coverage

Qualification Testing Environment

Session Information

Package List

Pull Request History

Pull Request 1947: Release v2.1.2

Pull Request 1945: PD > IPD and display site activation / participant enrollment in study info.

Pull Request 1942: gsm v2.1.2 release candidate

Pull Request 1941: Add act_fpfv and est_fpfv to STUDY.yaml spec

Pull Request 1932: Closes #1928 swaps out last remnants of kable and kableExtra in favor of gt

Pull Request 1931: Closes #1882 adds a toggle to display past year or full data

Pull Request 1930: Update Metrics.yaml to not generate lWorkflows within steps

Pull Request 1926: Fix country metadata

Pull Request 1923: Fix Ingest return value

Pull Request 1917: Keep bg color for switch.

Pull Request 1915: Add Nickname to report header and fix RunQuery bug

Pull Request 1913: updated class structure

Pull Request 1910: avoid column name conflicts between Groups and Results

Pull Request 1909: Release v2.1.1

Pull Request 1908: Fix country overview text

Pull Request 1907: Update rbm-viz.

Pull Request 1906: Embed necessary dependencies in Report_StudyInfo().

Pull Request 1904: Gsm v2.1.1 release candidate

Pull Request 1903: Fix overall group select bug.

Pull Request 1901: Closes #1890 and #1900 to properly check for dates and fix other bugs in checkSpec

Pull Request 1899: Closes #1880 add site/participant target numbers and labels to STUDY.yaml

Pull Request 1898: Flag colors

Pull Request 1897: Closes #1894 address bug in Input_Rate() for 0 row dataframe inputs for dfNumerator/dfDenominator

Pull Request 1892: Closes #1877 and #1883 addressing bugfixes related to StudyID on Report_Setup() and reportingXXXX datasets

Pull Request 1891: Only show flag-rows in Report_FlagOverTime()

Pull Request 1889: Resolve errors related to missing data and an incomplete set of MetricID in dfBounds .

Pull Request 1885: Make Report_StudyInfo() Friendlier to Shiny

Pull Request 1884: Closes #1659 and #1660 to use gt() instead of kbl() in our functions and reports

Pull Request 1876: Fix country report

Pull Request 1875: Closes #1872 fix miscellaneous aesthetics things and issues

Pull Request 1871: yes to true in yamls

Pull Request 1870: Release v2.1.0

Pull Request 1869: Closes #1863 address small bugs in MakeWorkflowList() run as intended

Pull Request 1867: Gsm v2.1.0 Release Candidate

Pull Request 1865: Workflow updates.

Pull Request 1864: Load/Save - Take 2

Pull Request 1862: Closes #1859 checks and updates qualification tests in test/testqualification to align with new workflows for v2.1.0 release

Pull Request 1861: Run {gsm} using local data store.

Pull Request 1856: Add rbm-viz v2.1.0.

Pull Request 1853: Discuss #1848 sections of package where there’s a difference of usage between gt vs “not”- gt

Pull Request 1852: Ingest modular

Pull Request 1851: Update checkSpec() cli message to handle _all required

Pull Request 1850: Closes #1653 adds Flag Over Time Widget to Study Overview as a tab

Pull Request 1849: MakeStudyInfo() function

Pull Request 1847: make analysis workflow work

Pull Request 1844: Add subjid to EDC domains in mapping workflow.

Pull Request 1843: MakeMetricTable()

Pull Request 1841: Refactor Data Ingestion Workflow

Pull Request 1839: skip Analysis_ checks in checkSpec

Pull Request 1833: Closes #1636 allows Visualize_Metric() to run on just results

Pull Request 1831: Closes #1728 Adds footnote to scatterplot widget

Pull Request 1829: Closes #1795 add assertions/stopifnot for widget inputs

Pull Request 1828: Update sample reporting data

Pull Request 1827: Add all required spec tables to workflows

Pull Request 1826: Update PR template

Pull Request 1824: Closes #1686 Renders a message in KRI_Report() when there are 0 rows in the summary table

Pull Request 1817: Cloes #1678 standardize use of cli_inform() and cli_warn()

Pull Request 1815: Closes #1779 Enhance CombineSpecs() with deduplication, enforcing required and adding checks for type

Pull Request 1814: Add type validation to CheckSpec()

Pull Request 1813: gsm extensions vignette

Pull Request 1812: Closes #1722 Study Status Table display bugfix of indiscriminant first five attributes

Pull Request 1932: Closes #1928 swaps out last remnants of `kable` and `kableExtra` in favor of `gt`

Pull Request 1930: Update `Metrics.yaml` to not generate `lWorkflows` within steps

Pull Request 1915: Add Nickname to report header and fix `RunQuery` bug

Pull Request 1910: avoid column name conflicts between `Groups` and `Results`

Pull Request 1899: Closes #1880 add site/participant target numbers and labels to `STUDY.yaml`

Pull Request 1897: Closes #1894 address bug in `Input_Rate()` for 0 row dataframe inputs for dfNumerator/dfDenominator

Pull Request 1892: Closes #1877 and #1883 addressing bugfixes related to `StudyID` on `Report_Setup()` and `reportingXXXX` datasets

Pull Request 1889: Resolve errors related to missing data and an incomplete set of `MetricID` in `dfBounds` .

Pull Request 1884: Closes #1659 and #1660 to use `gt()` instead of `kbl()` in our functions and reports

Pull Request 1869: Closes #1863 address small bugs in `MakeWorkflowList()` run as intended

Pull Request 1861: Run `{gsm}` using local data store.

Pull Request 1856: Add `rbm-viz` v2.1.0.

Pull Request 1853: Discuss #1848 sections of package where there’s a difference of usage between `gt` vs “not”- `gt`

Pull Request 1851: Update `checkSpec()` cli message to handle `_all` required

Pull Request 1844: Add `subjid` to EDC domains in mapping workflow.

Pull Request 1839: skip `Analysis_` checks in checkSpec

Pull Request 1833: Closes #1636 allows `Visualize_Metric()` to run on just results

Pull Request 1824: Closes #1686 Renders a message in `KRI_Report()` when there are 0 rows in the summary table

Pull Request 1817: Cloes #1678 standardize use of `cli_inform()` and `cli_warn()`

Pull Request 1815: Closes #1779 Enhance `CombineSpecs()` with deduplication, enforcing `required` and adding checks for `type`

Pull Request 1814: Add type validation to `CheckSpec()`

Pull Request 1808: Add `type` field and query columns to all `spec` s

Pull Request 1789: Add explicit snapshot date subset to `Widget_GroupOverview` .

Pull Request 1786: Use `required` param from `spec` in `CheckSpec()`

Pull Request 1775: update `analyticsInput` to match with `analyticsSummary`

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

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

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