Update Github actions

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^\.github$
 ^codecov\.yml$
+^doc$
+^Meta$

.github/workflows/R-CMD-check.yaml

@@ -47,15 +47,13 @@ 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")
-          devtools::load_all('../clindata')
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: rcmdcheck
+          devtools::install('../clindata')
+          devtools::install(dependencies=TRUE)
+          install.packages('rcmdcheck')
 
       - uses: r-lib/actions/check-r-package@v1
 

.github/workflows/test-coverage.yaml

@@ -15,16 +15,30 @@ 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
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: covr
+      - name: Clone clindata
+        run: |
+          cd ..
+          git clone git@github.com:Gilead-BioStats/clindata.git
+          cd gsm
+
+      - name: install packages
+        shell: Rscript {0}
+        run: |
+          install.packages("devtools")
+          devtools::install('../clindata')
+          devtools::install(dependencies=TRUE)
+          install.packages('covr')
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::package_coverage()
         shell: Rscript {0}

.gitignore

@@ -39,4 +39,7 @@ vignettes/*.pdf
 .Renviron
 .Rproj.user
 
-.DS_Store
+.DS_Store
+inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -17,10 +17,13 @@ Suggests:
     testthat (>= 3.0.0),
     safetyData,
     covr,
-    clindata
+    clindata,
+    knitr,
+    rmarkdown
 LazyData: true
+Remotes: 
+    phuse-org/valtools
 Roxygen: list(markdown = TRUE)
-Remotes:
-    Gilead-BioStats/clindata
 RoxygenNote: 7.1.2
 Config/testthat/edition: 3
+VignetteBuilder: knitr

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

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: