Try to get website to publish

.Rbuildignore

@@ -1,3 +1,15 @@
 ^ramnog\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^README.Rmd
+^_pkgdown.yml
+^docs
+^.vscode
+^.github
+^.githooks
+^.pre-commit-config.yaml
+RELEASE_BODY\.txt
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,83 @@
+# 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:
+ branches: [main, master, dev]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+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: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::.
+ needs: website
+
+ - name: Build site
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
+
+ # If not pull request a brand new webpage is deployed
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/github-pages-deploy-action@v4.5.0
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
+
+ # If pull request the webpage is deployed inside a dev/"PR number" folder for review
+ - name: Add pkgdown PR Comment
+ uses: marocchino/sticky-pull-request-comment@v2
+ if: github.event_name == 'pull_request'
+ with:
+ recreate: true
+ header: pkgdown
+ message: |
+ # Github pages
+ Review the pkgdown webpage for the PR [here](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/dev/${{ github.event.pull_request.number }})
+
+ - name: Copy page to temp folder
+ if: github.event_name == 'pull_request'
+ run: |
+ mkdir -p /home/runner/work/dev
+ cp -r ./docs/* /home/runner/work/dev
+
+ - name: Check out gh-pages branch
+ if: github.event_name == 'pull_request'
+ uses: actions/checkout@v4
+ with:
+ ref: gh-pages
+
+ - name: Copy and push to gh-pages
+ if: github.event_name == 'pull_request'
+ run: |
+ mkdir -p dev/${{ github.event.pull_request.number }}
+ cp -r /home/runner/work/dev/* ./dev/${{ github.event.pull_request.number }}
+ git config --global user.email "actions-robot@novonordisk.com"
+ git config --global user.name "Actions Robot From Github Actions"
+ git add .
+ git commit -m "Update gh pages from the PR"
+ git push

.gitignore

@@ -1,3 +1,6 @@
 .Rproj.user
 inst/doc
 docs/
+launch.json
+.Rhistory
+docs

DESCRIPTION

@@ -10,20 +10,27 @@ Description: What the package does (one paragraph).
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 Imports:
+ data.table (>= 1.14.2),
+Suggests:
  chef,
  chefCriteria,
  chefStats,
- data.table (>= 1.14.2),
-Suggests: 
  knitr,
+ targets,
+ usethis,
  rmarkdown,
  testthat (>= 3.0.0),
- kableExtra (>= 1.4)
+ kableExtra (>= 1.4),
+ testr,
+ tidyr,
+ pharmaverseadam
+Config/testthat/edition: 3
 Remotes:
+ hta-pharma/chefStats,
  hta-pharma/chef,
  hta-pharma/chefCriteria,
- hta-pharma/chefStats
-Config/testthat/edition: 3
+ matthew-phelps/testr
 VignetteBuilder: knitr
+URL: https://hta-pharma.github.io/ramnog/

NAMESPACE

@@ -1,4 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
-export(mk_adae_demo)
+export(dummy_fn)
 import(data.table)

R/dummy_fn.R

@@ -0,0 +1,9 @@
+#' Title
+#' @description exists only to import data.table
+#' @return Nothing.
+#' @export
+#'
+#' @import data.table
+dummy_fn <- function(){
+
+}

_pkgdown.yml

@@ -1,16 +1,10 @@
-url: ~
+url: https://hta-pharma.github.io/ramnog/
 template:
  bootstrap: 5
-
-
-
 articles:
-
 - title: Overview
  navbar: Overview
- contents:
- - ep_overview
-
+ contents: ep_overview
 - title: Endpoint Population and Outcome Specification
  navbar: Endpoint Population and Outcome Specification
  contents:
@@ -20,29 +14,21 @@ articles:
  - ep_spec_event_def
  - ep_spec_strata_def
  - ep_spec_label
-
 - title: Endpoint Statistics
  navbar: Endpoint Statistics
- contents:
- - starts_with('methods_')
-
+ contents: starts_with('methods_')
 - title: Endpoint Results
  navbar: Endpoint Results
- contents:
- - starts_with("results")
-
+ contents: starts_with("results")
 - title: Endpoint Examples
  navbar: Endpoint Examples
- contents:
- - starts_with("example_")
-
+ contents: starts_with("example_")
 - title: Debugging
  navbar: Debugging
- contents:
- - debugging
-
+ contents: debugging
 - title: Development
  navbar: Development
  contents:
  - starts_with("dev")
  - validation
+

tests/testthat/_snaps/mild_ae_by_sex.md

@@ -1,13 +1,14 @@
 # Complex pipeline runs without errors
 
  Code
- ep_stat[, .(stat_filter, endpoint_group_filter, label, description, qualifiers,
- value)]
+ ep_stat[, .(stat_filter, endpoint_group_filter, stat_result_label,
+ stat_result_description, stat_result_qualifiers, stat_result_value)]
  Output
  stat_filter
+ <char>
  1: TOTAL_ == "total" & TRT01A == "Placebo"
- 2: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
- 3:  TOTAL_ == "total" & TRT01A == "Placebo"
+ 2:  TOTAL_ == "total" & TRT01A == "Placebo"
+ 3: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
  4: TOTAL_ == "total" & TRT01A == "Xanomeline High Dose"
  5: SEX == "F" & TRT01A == "Placebo"
  --- 
@@ -17,6 +18,7 @@
  4277: 
  4278: 
  endpoint_group_filter
+ <char>
  1: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
  2: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
  3: AESOC == "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS" & AESEV == "MILD"
@@ -28,16 +30,30 @@
  4276: AESOC == "EAR AND LABYRINTH DISORDERS" & AESEV == "SEVERE"
  4277: AESOC == "NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)" & AESEV == "SEVERE"
  4278: AESOC == "NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)" & AESEV == "SEVERE"
- label description qualifiers value
- 1: E Number of events <NA> 36
- 2: E Number of events <NA> 75
- 3: N Number of subjects <NA> 86
- 4: N Number of subjects <NA> 72
- 5: E Number of events <NA> 18
- --- 
- 4274: <NA> P-value interaction not conducted <NA> NA
- 4275: <NA> P-value interaction not conducted <NA> NA
- 4276: <NA> P-value interaction not conducted <NA> NA
- 4277: <NA> P-value interaction not conducted <NA> NA
- 4278: <NA> P-value interaction not conducted <NA> NA
+ stat_result_label stat_result_description
+ <char> <char>
+ 1: E Number of events
+ 2: N Number of subjects
+ 3: E Number of events
+ 4: N Number of subjects
+ 5: E Number of events
+ --- 
+ 4274: <NA> P-value interaction not conducted
+ 4275: <NA> P-value interaction not conducted
+ 4276: <NA> P-value interaction not conducted
+ 4277: <NA> P-value interaction not conducted
+ 4278: <NA> P-value interaction not conducted
+ stat_result_qualifiers stat_result_value
+ <char> <num>
+ 1: <NA> 36
+ 2: <NA> 86
+ 3: <NA> 75
+ 4: <NA> 72
+ 5: <NA> 18
+ --- 
+ 4274: <NA> NA
+ 4275: <NA> NA
+ 4276: <NA> NA
+ 4277: <NA> NA
+ 4278: <NA> NA
 

tests/testthat/binary_type_2.R

@@ -23,7 +23,7 @@ test_that("Binary outcomes of type 2 work", {
  mk_adam_fn = list(mk_adae),
  )
  # ACT ---------------------------------------------------------------------
- browser()
+
  targets::tar_make()
  targets::tar_load(ep_stat)
 

tests/testthat/test-binary_type_2.R

@@ -27,6 +27,5 @@ test_that("multiplication works", {
  # ACT ---------------------------------------------------------------------
  targets::tar_make()
  targets::tar_load(ep_stat)
- browser()
 
 })

tests/testthat/test-demographics.R

@@ -44,6 +44,7 @@ test_that("Demographics work with other endpoints", {
  mk_adam_fn = list(mk_adae, mk_advs),
  )
  # ACT ---------------------------------------------------------------------
+
  targets::tar_make()
  targets::tar_load(ep_stat)
 
@@ -54,7 +55,7 @@ test_that("Demographics work with other endpoints", {
  actual <-
  ep_stat[endpoint_group_filter == "AESOC == \"SOCIAL CIRCUMSTANCES\" & AESEV == \"SEVERE\"" &
  fn_name == "RR" &
- stat_filter == "SEX == \"F\""& label == "RR", value]
+ stat_filter == "SEX == \"F\"" & stat_result_label == "RR", "stat_result_value"]
  x1 <- x[SEX == "F" & SAFFL == "Y"]
  x1[AESOC == "SOCIAL CIRCUMSTANCES" &
  AESEV == "SEVERE", event := TRUE]
@@ -65,12 +66,16 @@ test_that("Demographics work with other endpoints", {
  c <- 0.5 # No outcome, not exposed
  d <- 53.5 # No outcome, not exposed
  expected <- (a / sum(a, b)) / (c / sum(c, d))
- expect_identical(actual, expected)
+ expect_identical(actual$stat_result_value, expected)
 
  # Spot check the Demographic stats
  x <- mk_advs()
+ a <-
+ ep_stat[stat_result_qualifiers == "SEX" &
+ stat_result_label == "n_missing"] |> data.table::setorder(stat_filter)
+ expected <- x[is.na(SEX), .N, by = .(TRT01A)] |> data.table::setorder(TRT01A)
 
- a <- ep_stat[qualifiers=="SEX"&label=="n_missing"] |> setorder(stat_filter)
- expected <- x[is.na(SEX), .N, by=.(TRT01A)] |> setorder(TRT01A)
- expect_equal(a$value, expected$N)
+ expect_equal(a$stat_result_value |> as.integer(), as.integer(expected$N))
 })
+
+

tests/testthat/test-empty_strata_level.R

@@ -44,6 +44,6 @@ test_that("stat funtion that produces a 0 returns result ",
 
 
  actual <-
- ep_stat[grepl("Placebo", stat_filter), value]
+ ep_stat[grepl("Placebo", stat_filter), stat_result_value]
  expect_equal(actual, 0)
  })