From 48f605d8004f15362a25ca2d21f3bf226dfc3486 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 9 Feb 2022 15:58:54 -0500 Subject: [PATCH 1/9] try different coverage calc. #58 --- .github/workflows/test-coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index d403d847c..53a33e325 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -26,5 +26,5 @@ jobs: extra-packages: covr - name: Test coverage - run: covr::codecov() + run: covr::package_coverage() shell: Rscript {0} From 38a066ac18581b527a157936f41fb4ca50518d2e Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 9 Feb 2022 17:45:18 -0500 Subject: [PATCH 2/9] load clindata --- .github/workflows/test-coverage.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 53a33e325..17275d981 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -15,12 +15,28 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: + - uses: webfactory/ssh-agent@v0.5.4 + with: + ssh-private-key: ${{ secrets.LOAD_CLINDATA }} + - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@v1 with: use-public-rspm: true + - name: Clone clindata + run: | + cd .. + git clone git@github.com:Gilead-BioStats/clindata.git + cd gsm + + - name: load clindata + shell: Rscript {0} + run: | + install.packages("devtools") + devtools::load_all('../clindata') + - uses: r-lib/actions/setup-r-dependencies@v1 with: extra-packages: covr From cc8662f67163c1044b2722960d5099c755b97eee Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Wed, 9 Feb 2022 17:59:27 -0500 Subject: [PATCH 3/9] tweak 1 of x --- .github/workflows/test-coverage.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 17275d981..69ef7fa92 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -35,11 +35,9 @@ jobs: shell: Rscript {0} run: | install.packages("devtools") - devtools::load_all('../clindata') - + devtools::install('../clindata') + - uses: r-lib/actions/setup-r-dependencies@v1 - with: - extra-packages: covr - name: Test coverage run: covr::package_coverage() From a13ac91821de4b9ba09968159c306427eead9d9c Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 10 Feb 2022 09:26:55 -0500 Subject: [PATCH 4/9] tweak 2 of x --- .github/workflows/R-CMD-check.yaml | 8 +++----- .github/workflows/test-coverage.yaml | 4 ++-- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 784c639ce..52111a7c7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -51,11 +51,9 @@ jobs: shell: Rscript {0} run: | install.packages("devtools") - devtools::load_all('../clindata') - - - uses: r-lib/actions/setup-r-dependencies@v1 - with: - extra-packages: rcmdcheck + devtools::install('../clindata') + devtools::install() + install.packages('rcmdcheck') - uses: r-lib/actions/check-r-package@v1 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 69ef7fa92..e65113897 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -36,8 +36,8 @@ jobs: run: | install.packages("devtools") devtools::install('../clindata') - - - uses: r-lib/actions/setup-r-dependencies@v1 + devtools::install() + install.packages('covr') - name: Test coverage run: covr::package_coverage() From 620d413499cc798b3be7bd2ddca904d0b00d4ecb Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 10 Feb 2022 09:35:11 -0500 Subject: [PATCH 5/9] tweak 3 of x --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/test-coverage.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 52111a7c7..0fcccb248 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -52,7 +52,7 @@ jobs: run: | install.packages("devtools") devtools::install('../clindata') - devtools::install() + devtools::install(dependencies=TRUE) install.packages('rcmdcheck') - uses: r-lib/actions/check-r-package@v1 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index e65113897..adb1137e6 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -36,7 +36,7 @@ jobs: run: | install.packages("devtools") devtools::install('../clindata') - devtools::install() + devtools::install(dependencies=TRUE) install.packages('covr') - name: Test coverage From 51ed59d5243bee51de8eab4087eab60ec126d1f7 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 10 Feb 2022 11:54:55 -0500 Subject: [PATCH 6/9] tweak title --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/test-coverage.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0fcccb248..5d1bebd7e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -47,7 +47,7 @@ jobs: git clone git@github.com:Gilead-BioStats/clindata.git cd gsm - - name: load clindata + - name: install packages shell: Rscript {0} run: | install.packages("devtools") diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index adb1137e6..775fa0a5c 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -31,7 +31,7 @@ jobs: git clone git@github.com:Gilead-BioStats/clindata.git cd gsm - - name: load clindata + - name: install packages shell: Rscript {0} run: | install.packages("devtools") From bdee5ee7fc5e963bbf33491a19395ac86c7491ec Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 10 Feb 2022 13:15:35 -0500 Subject: [PATCH 7/9] remove clindata remote --- DESCRIPTION | 2 -- 1 file changed, 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 06298a43a..c4008b413 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,5 @@ Suggests: clindata LazyData: true Roxygen: list(markdown = TRUE) -Remotes: - Gilead-BioStats/clindata RoxygenNote: 7.1.2 Config/testthat/edition: 3 From 92e0c518470005bf2a5bf83fbd05b3cb0135aa48 Mon Sep 17 00:00:00 2001 From: Jeremy Wildfire Date: Thu, 10 Feb 2022 13:37:44 -0500 Subject: [PATCH 8/9] add remote for valtools. fix #125 --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index c4008b413..899ba9a67 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,6 +19,8 @@ Suggests: covr, clindata LazyData: true +Remotes: + phuse-org/valtools Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 Config/testthat/edition: 3 From 10d63392189f0ca68d675ec532138a0db9a8bb64 Mon Sep 17 00:00:00 2001 From: Nathan Kosiba Date: Fri, 11 Feb 2022 13:19:12 +0000 Subject: [PATCH 9/9] add gsm vignette --- .Rbuildignore | 2 ++ .gitignore | 5 ++++- DESCRIPTION | 5 ++++- vignettes/.gitignore | 2 ++ vignettes/gsm.Rmd | 23 +++++++++++++++++++++++ 5 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 vignettes/.gitignore create mode 100644 vignettes/gsm.Rmd diff --git a/.Rbuildignore b/.Rbuildignore index df38fde24..17be840ac 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,3 +2,5 @@ ^\.Rproj\.user$ ^\.github$ ^codecov\.yml$ +^doc$ +^Meta$ diff --git a/.gitignore b/.gitignore index 4211e783f..52d114696 100644 --- a/.gitignore +++ b/.gitignore @@ -39,4 +39,7 @@ vignettes/*.pdf .Renviron .Rproj.user -.DS_Store \ No newline at end of file +.DS_Store +inst/doc +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 06298a43a..1041a62d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,10 +17,13 @@ Suggests: testthat (>= 3.0.0), safetyData, covr, - clindata + clindata, + knitr, + rmarkdown LazyData: true Roxygen: list(markdown = TRUE) Remotes: Gilead-BioStats/clindata RoxygenNote: 7.1.2 Config/testthat/edition: 3 +VignetteBuilder: knitr diff --git a/vignettes/.gitignore b/vignettes/.gitignore new file mode 100644 index 000000000..097b24163 --- /dev/null +++ b/vignettes/.gitignore @@ -0,0 +1,2 @@ +*.html +*.R diff --git a/vignettes/gsm.Rmd b/vignettes/gsm.Rmd new file mode 100644 index 000000000..ec2e0bf93 --- /dev/null +++ b/vignettes/gsm.Rmd @@ -0,0 +1,23 @@ +--- +title: "Getting Started" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Getting Started} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +```{r setup} +library(gsm) +``` + +Gilead Statistical Monitoring {gsm} R package + +The Gilead Statistical Monitoring or {gsm} R package provides a framework for statistical data monitoring using R and Shiny. The provides a framework that allows users to assess, visualize and explore clinical trial data, allowing users to detect issues at sites, identify the root cause and decide on the appropriate action. The package currently provides asessments for the following domains: