Trying to get github pages working

.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 +1,49 @@
+# 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}
+
+      - 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
+

.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)
           })

tests/testthat/test-mild_ae_by_sex.R

@@ -34,13 +34,13 @@ test_that("Complex pipeline runs without errors",
             targets::tar_make()
 
             # EXPECT ------------------------------------------------------------------
-            x <- targets::tar_meta() %>% data.table::as.data.table()
+            x <- targets::tar_meta() |> data.table::as.data.table()
             targets::tar_load(ep_stat)
             expect_true(all(is.na(x$error)))
             expect_snapshot(ep_stat[, .(stat_filter,
                                         endpoint_group_filter,
-                                        label,
-                                        description,
-                                        qualifiers,
-                                        value)])
+                                        stat_result_label,
+                                        stat_result_description,
+                                        stat_result_qualifiers,
+                                        stat_result_value)])
           })