Add examples, vignettes and reports to pkgdown site

.github/workflows/pkgdown.yaml

@@ -1,27 +1,20 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  push:
-    branches: [main, master]
   pull_request:
-  release:
-    types: [published]
+    branches: [main, dev]
+  push:
+    branches: [main]
   workflow_dispatch:
 
-name: pkgdown.yaml
-
-permissions: read-all
+name: pkgdown
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
       contents: write
+
     steps:
       - uses: actions/checkout@v4
 
@@ -33,17 +26,54 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown
           needs: website
 
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+      - name: Generate sample reports
         shell: Rscript {0}
+        run: |
+          install.packages(c("devtools", "here"))
+          devtools::load_all()
+          dir.create(here::here("pkgdown", "assets"), recursive = TRUE)
+          library(gsm.kri)
+          library(gsm.core)
 
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+          lCharts <- gsm.kri::MakeCharts(
+            dfResults = gsm.core::reportingResults,
+            dfGroups = gsm.core::reportingGroups,
+            dfMetrics = gsm.core::reportingMetrics,
+            dfBounds = gsm.core::reportingBounds
+          )
+
+          gsm.kri::Report_KRI(
+            lCharts = lCharts,
+            dfResults =  gsm.kri::FilterByLatestSnapshotDate(gsm.core::reportingResults),
+            dfGroups =  gsm.core::reportingGroups,
+            dfMetrics = gsm.core::reportingMetrics,
+            strOutputDir = here::here("pkgdown", "assets"),
+            strOutputFile = "report_kri_site.html"
+          )
+
+          ## Country Report
+            lCharts_country <- gsm.kri::MakeCharts(
+            dfResults = gsm.core::reportingResults_country,
+            dfGroups = gsm.core::reportingGroups_country,
+            dfMetrics = gsm.core::reportingMetrics_country,
+            dfBounds = gsm.core::reportingBounds_country
+          )
+
+          gsm.kri::Report_KRI(
+            lCharts = lCharts_country,
+            dfResults =  gsm.kri::FilterByLatestSnapshotDate(gsm.core::reportingResults_country),
+            dfGroups =  gsm.core::reportingGroups_country,
+            dfMetrics = gsm.core::reportingMetrics_country,
+            strOutputDir = here::here("pkgdown", "assets"),
+            strOutputFile = "report_kri_country.html"
+          )
+
+
+      - name: Deploy pkgdown
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(install = T)'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: openrbqm
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Version: 0.0.1
 Authors@R: c(
     person("Jeremy", "Wildfire", email = "jwildfire@gmail.com", role = c("aut", "cre")),
     person("Laura", "Maxwell", email = "lkmaxwell23@gmail.com", role = c("aut"))
@@ -23,15 +23,17 @@ Imports:
     rstudioapi,
     utils
 Remotes:
-    gsm.core=Gilead-BioStats/gsm.core@main,
+    gsm.core=Gilead-BioStats/gsm.core@v1.1.0,
     gsm.app=Gilead-BioStats/gsm.app,
-    gsm.datasim=Gilead-BioStats/gsm.datasim@dev,
-    gsm.kri=Gilead-BioStats/gsm.kri@main,
-    gsm.mapping=Gilead-BioStats/gsm.mapping@main,
-    gsm.reporting=Gilead-BioStats/gsm.reporting@main,
-    gsm.qc=Gilead-BioStats/gsm.qc@main
+    gsm.datasim=Gilead-BioStats/gsm.datasim@v1.0.0,
+    gsm.kri=Gilead-BioStats/gsm.kri@v1.1.0,
+    gsm.mapping=Gilead-BioStats/gsm.mapping@v1.0.1,
+    gsm.reporting=Gilead-BioStats/gsm.reporting@v1.0.1,
+    gsm.qc=Gilead-BioStats/gsm.qc@v1.0.1
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    DT,
+    gt
 VignetteBuilder: knitr
 URL: https://openrbqm.github.io/openrbqm/

R/attach.R

@@ -70,10 +70,6 @@ openrbqm_detach <- function() {
 
 #' List all packages imported by openrbqm
 #'
-#' @export
-#'
-#' @examples
-#' #openrbqm_packages()
 openrbqm_packages <- function() {
   # get all imports from openrbqm's package description file
   raw <- utils::packageDescription("openrbqm")$Imports

README.md

@@ -10,50 +10,4 @@ Collection of R Packages designed for Risk Based Quality Management
 5. gsm.reporting
 6. gsm.app
 7. gsm.template
-8. grail
 9. gsm.datasim
-
-
-## Requirements before `{openrbqm}` v1.0.0 release
-
-### Critical outstanding issues
-
-#### Overview 
-
-- [ ] `{gsm.reporting}` repo needs to be created and reporting functions and workflows be migrated
-- [ ] `{gsm.core}` stripped down after mapping, kri and reporting repo contents confirmed and with at least one release.
-  - [ ] all examples and most vignettes moved to  `{openrbqm}`
-- [ ] `{gsm.mapping}` v1.0.0 release candidate with stripped `{gsm}` dev version (or `{gsm.core}` v2.3.0-rc) as dependency
-- [ ] `{gsm.kri}` v1.0.0 release candidate with `{gsm.mapping}` v1.0.0-rc and stripped `{gsm.core}` v2.3.0-rc as dependencies
-- [ ] `{gsm.endpoints}` mapping edits
-  - [ ] direct from raw mapping yamls moved to `{gsm.mapping}` with more specific file names
-  - [ ] update dependencies appropriately
-
-#### Detailed outstanding issues
-
-- `{gsm.core}` issues
-  - [ ] [Feature: Migrate Mapping components to gsm.mapping](https://github.com/Gilead-BioStats/gsm/issues/1972)
-    - available on gsm branch `fix-1972v2` in this [PR](https://github.com/Gilead-BioStats/gsm/pull/2002)
-  - [ ] [Feature: Remove gsm.kri functions, workflows and tests](https://github.com/Gilead-BioStats/gsm/issues/2013)
-    - available on gsm branch `fix-2013`
-  - [ ] [Feature: Ensure all workflows are migrated to their respective packages](https://github.com/Gilead-BioStats/gsm/issues/2014)
-  - [ ] [Feature: Migrate reporting vignette to {gsm.reporting}](https://github.com/Gilead-BioStats/gsm/issues/2015)
-  - [ ] [Feature: Migrate vignettes to {openrbqm} package](https://github.com/Gilead-BioStats/gsm/issues/2016)
-  - [ ] [Feature: Migrate workflow/reporting qualification tests to {gsm.kri}](https://github.com/Gilead-BioStats/gsm/issues/2017)
-  - [ ] [QC: remove util- prefix in file names](https://github.com/Gilead-BioStats/gsm/issues/2026)
-- `{gsm.mapping}` issues
-  - [x] [Write a vignette and template for how to request a new domain/variable](https://github.com/Gilead-BioStats/gsm.mapping/issues/4)
-  - [ ] [Write a vignette displaying all mapped dfs and variables ](https://github.com/Gilead-BioStats/gsm.mapping/issues/3)
-    - Begun, and merged into dev via PR #18, but needs some editing to fully address the issue
-- `{gsm.kri}` issues
-  - [ ] [Migrate Vignettes and make pkgdown site](https://github.com/Gilead-BioStats/gsm.kri/issues/9)
-    - begun on gsm branch `fix-9`
-- `{gsm.endpoints}` issues
-  - [ ] [Feature: Move rawplus mapping yamls to the gsm.mapping package](https://github.com/Gilead-BioStats/gsm.endpoints/issues/134)
-  - [ ] [Feature: Update names and meta information of workflows to be more specific](https://github.com/Gilead-BioStats/gsm.endpoints/issues/133)
-- `{gsm.reporting}` issues
-
-### Nice to haves
-- `{gsm.template}` issues
-- `{gsm.datasim}` issues
-  - add `{gsm.endpoints}` domains to available data and vars. [(Issue here)](https://github.com/Gilead-BioStats/gsm.datasim/issues/34)

_pkgdown.yml

@@ -7,4 +7,11 @@ navbar:
   structure:
     left: [articles, Reports, reference, news]
     right: [search, github]
-
+  components:
+    Reports:
+      text: Sample Reports
+      menu:
+        - text: Site Report
+          href: report_kri_site.html
+        - text: Country Report
+          href: report_kri_country.html

inst/examples/1_AdverseEventKRI.R

@@ -0,0 +1,55 @@
+#### Example 1.1 - Generate an Adverse Event Metric using the standard {gsm.core} workflow
+
+dfInput <- Input_Rate(
+  dfSubjects= gsm.core::lSource$Raw_SUBJ,
+  dfNumerator= gsm.core::lSource$Raw_AE,
+  dfDenominator = gsm.core::lSource$Raw_SUBJ,
+  strSubjectCol = "subjid",
+  strGroupCol = "siteid",
+  strNumeratorMethod= "Count",
+  strDenominatorMethod= "Sum",
+  strDenominatorCol= "timeonstudy"
+)
+
+dfTransformed <- Transform_Rate(dfInput)
+dfAnalyzed <- Analyze_NormalApprox(dfTransformed, strType = "rate")
+dfFlagged <- Flag_NormalApprox(dfAnalyzed, vThreshold = c(-3,-2,2,3))
+dfSummarized <- Summarize(dfFlagged)
+
+table(dfSummarized$Flag)
+
+#### Example 1.2 - Make an SAE Metric by adding a filter.  Also works with pipes.
+
+SAE_KRI <- Input_Rate(
+  dfSubjects= gsm.core::lSource$Raw_SUBJ,
+  dfNumerator= gsm.core::lSource$Raw_AE %>% filter(aeser=="Y"),
+  dfDenominator = gsm.core::lSource$Raw_SUBJ,
+  strSubjectCol = "subjid",
+  strGroupCol = "siteid",
+  strNumeratorMethod= "Count",
+  strDenominatorMethod= "Sum",
+  strDenominatorCol= "timeonstudy"
+) %>%
+  Transform_Rate %>%
+  Analyze_NormalApprox(strType = "rate") %>%
+  Flag_NormalApprox(vThreshold = c(-3,-2,2,3)) %>%
+  Summarize
+
+table(SAE_KRI$Flag)
+
+### Example 1.3 - Visualize Metric distribution using Bar Charts using provided htmlwidgets
+library(gsm.kri)
+
+labels <- list(
+  Metric= "Serious Adverse Event Rate",
+  Numerator= "Serious Adverse Events",
+  Denominator= "Days on Study"
+)
+
+gsm.kri::Widget_BarChart(dfResults = SAE_KRI, lMetric=labels, strOutcome="Metric")
+gsm.kri::Widget_BarChart(dfResults = SAE_KRI, lMetric=labels, strOutcome="Score")
+gsm.kri::Widget_BarChart(dfResults = SAE_KRI, lMetric=labels, strOutcome="Numerator")
+
+### Example 1.4 - Create Scatter plot with confidence bounds
+dfBounds <- Analyze_NormalApprox_PredictBounds(SAE_KRI, vThreshold = c(-3,-2,2,3))
+gsm.kri::Widget_ScatterPlot(SAE_KRI, lMetric = labels, dfBounds = dfBounds)

inst/examples/2_AdverseEventWorkflow.R

@@ -0,0 +1,128 @@
+library(gsm.mapping)
+library(gsm.kri)
+
+#### Example 2.1 - Configurable Adverse Event Workflow
+
+# Define YAML workflow
+AE_workflow <- read_yaml(text=
+'meta:
+  Type: Analysis
+  ID: kri0001
+  GroupLevel: Site
+  Abbreviation: AE
+  Metric: Adverse Event Rate
+  Numerator: Adverse Events
+  Denominator: Days on Study
+  Model: Normal Approximation
+  Score: Adjusted Z-Score
+  AnalysisType: rate
+  Threshold: -2,-1,2,3
+  nMinDenominator: 30
+spec:
+  Mapped_AE:
+    subjid:
+      type: character
+  Mapped_SUBJ:
+    subjid:
+      type: character
+    invid:
+      type: character
+    timeonstudy:
+      type: integer
+steps:
+  - output: vThreshold
+    name: ParseThreshold
+    params:
+      strThreshold: Threshold
+  - output: Analysis_Input
+    name: Input_Rate
+    params:
+      dfSubjects: Mapped_SUBJ
+      dfNumerator: Mapped_AE
+      dfDenominator: Mapped_SUBJ
+      strSubjectCol: subjid
+      strGroupCol: invid
+      strGroupLevel: GroupLevel
+      strNumeratorMethod: Count
+      strDenominatorMethod: Sum
+      strDenominatorCol: timeonstudy
+  - output: Analysis_Transformed
+    name: Transform_Rate
+    params:
+      dfInput: Analysis_Input
+  - output: Analysis_Analyzed
+    name: Analyze_NormalApprox
+    params:
+      dfTransformed: Analysis_Transformed
+      strType: AnalysisType
+  - output: Analysis_Flagged
+    name: Flag_NormalApprox
+    params:
+      dfAnalyzed: Analysis_Analyzed
+      vThreshold: vThreshold
+  - output: Analysis_Summary
+    name: Summarize
+    params:
+      dfFlagged: Analysis_Flagged
+      nMinDenominator: nMinDenominator
+  - output: lAnalysis
+    name: list
+    params:
+      ID: ID
+      Analysis_Input: Analysis_Input
+      Analysis_Transformed: Analysis_Transformed
+      Analysis_Analyzed: Analysis_Analyzed
+      Analysis_Flagged: Analysis_Flagged
+      Analysis_Summary: Analysis_Summary
+')
+
+# Run the workflow
+lMappingWorkflows <- MakeWorkflowList(
+  c("AE", "SUBJ"),
+  strPath = here::here("tests/testthat/testdata/mappings"),
+  bExact = TRUE
+)
+mappings_spec <- gsm.mapping::CombineSpecs(lMappingWorkflows)
+lRawData <- gsm.mapping::Ingest(gsm.core::lSource, mappings_spec)
+AE_data <-list(
+  Mapped_SUBJ= lRawData$Raw_SUBJ,
+  Mapped_AE= lRawData$Raw_AE
+)
+AE_KRI <- RunWorkflow(lWorkflow = AE_workflow, lData = AE_data)
+
+# Create Barchart from workflow
+Widget_BarChart(dfResults = AE_KRI$Analysis_Summary)
+
+#### Example 2.2 - Run Country-Level Metric
+AE_country_workflow <- AE_workflow
+AE_country_workflow$meta$GroupLevel <- "Country"
+AE_country_workflow$steps[[2]]$params$strGroupCol <- "country"
+
+AE_country_KRI <- RunWorkflow(lWorkflow = AE_country_workflow, lData = AE_data)
+gsm.kri::Widget_BarChart(dfResults = AE_country_KRI$Analysis_Summary, lMetric = AE_country_workflow$meta)
+
+#### Example 2.3 - Create SAE workflow
+
+# Tweak AE workflow metadata
+SAE_workflow <- AE_workflow
+SAE_workflow$meta$File <- "SAE_KRI"
+SAE_workflow$meta$Metric <- "Serious Adverse Event Rate"
+SAE_workflow$meta$Numerator <- "Serious Adverse Events"
+
+# Add a step to filter out non-serious AEs `RunQuery`
+filterStep <- list(list(
+  name = "RunQuery",
+  output = "Mapped_AE",
+  params= list(
+    df= "Mapped_AE",
+    strQuery = "SELECT * FROM df WHERE aeser = 'Y'"
+  ))
+)
+SAE_workflow$steps <- SAE_workflow$steps %>% append(filterStep, after=0)
+
+# Run the updated workflow
+SAE_KRI <- RunWorkflow(lWorkflow = SAE_workflow, lData = AE_data )
+gsm.kri::Widget_BarChart(dfResults = SAE_KRI$Analysis_Summary, lMetric = SAE_workflow$meta)
+
+
+