Merge branch 'why-it-works-vignette' of https://github.com/SamuelBran…

…d1/primarycensoreddist into why-it-works-vignette

.Rbuildignore

@@ -25,3 +25,4 @@
 ^vignettes/using-stan-tools\.Rmd$
 ^vignettes/fitting-dists-with-stan\.Rmd$
 ^inst/pcens_model$
+^touchstone$

.github/workflows/benchmarks-comment.yaml

@@ -0,0 +1,20 @@
+name: Benchmarks (Comment)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  workflow_run:
+    workflows:
+      - Benchmarks
+    types:
+      - completed
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seabbs/touchstone/actions/comment@main
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/benchmarks.yaml

@@ -0,0 +1,81 @@
+name: Benchmarks
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    paths:
+      # Directories with source code and benchmarking code
+      - "inst/stan/**"
+      - "R/**"
+      - "src/**"
+      - "touchstone/**"
+      # Stan model
+      - "inst/pcens_model.stan"
+      # Benchmarking config file
+      - ".github/workflows/benchmarks*.yaml"
+      # Benchmarking action
+      - ".github/actions/touchstone-recieve/**"
+      # Package metadata
+      - DESCRIPTION
+  workflow_dispatch:
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      config: ${{ steps.read_touchstone_config.outputs.config }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - id: read_touchstone_config
+        run: |
+          content=`cat ./touchstone/config.json`
+          # the following lines are only required for multi line json
+          content="${content//'%'/'%25'}"
+          content="${content//$'\n'/'%0A'}"
+          content="${content//$'\r'/'%0D'}"
+          # end of optional handling for multi line json
+          echo "::set-output name=config::$content"
+  build:
+    needs: prepare
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - ${{ fromJson(needs.prepare.outputs.config) }}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
+
+      - name: Install cmdstanr
+        run: install.packages("cmdstanr")
+        shell: Rscript {0}
+
+      - name: Install cmdstan
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
+
+      - uses: seabbs/touchstone/actions/receive@main
+        with:
+          cache-version: 1
+          touchstone_ref: '@f5c859e'
+          benchmarking_repo: ${{ matrix.config.benchmarking_repo }}
+          benchmarking_ref: ${{ matrix.config.benchmarking_ref }}
+          benchmarking_path: ${{ matrix.config.benchmarking_path }}
+          extra-repositories: 'https://stan-dev.r-universe.dev'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: primarycensoreddist
 Title: Primary Event Censored Distributions in R and Stan
-Version: 0.3.0.1000
+Version: 0.4.0.1000
 Authors@R:
   c(person(given = "Sam",
            family = "Abbott",

NEWS.md

@@ -1,4 +1,14 @@
-# primarycensoreddist 0.3.0.1000
+# primarycensoreddist 0.4.0.1000
+
+This is the current development version.
+
+## Package
+
+* Add `{touchstone}` based benchmarks for benchmarking R utility functions, and fitting the `stan` and `fitdistplus` models.
+
+# primarycensoreddist 0.4.0
+
+In this release, we have added a new package `stan` model for fitting distributions using the `cmdstanr` package. We have also added a new function `fitdistdoublecens()` to allow for fitting of double censored and truncated data using the `fitdistrplus` package. As well as these functionality improvements this release focuses on improving the stability of the `stan` model and improving the speed of the `primary_censored_ode` function.
 
 ## Package
 

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/epinowcast/primarycensoreddist/",
   "issueTracker": "https://github.com/epinowcast/primarycensoreddist/issues/",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.3.0.1000",
+  "version": "0.4.0.1000",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -167,7 +167,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "296.764KB",
+  "fileSize": "343.237KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

touchstone/.gitignore

@@ -0,0 +1,6 @@
+*
+!script.R
+!config.json
+!.gitignore
+!header.R
+!footer.R

touchstone/config.json

@@ -0,0 +1,5 @@
+{
+  "os": "ubuntu-latest",
+  "r": "release",
+  "rspm": "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
+}

touchstone/footer.R

@@ -0,0 +1,10 @@
+# You can modify the PR comment footer here. You can use github markdown e.g.
+# emojis like :tada:.
+# This file will be parsed and evaluate within the context of
+# `benchmark_analyze` and should return the comment text as the last value.
+# See `?touchstone::pr_comment`
+link <- "https://lorenzwalthert.github.io/touchstone/articles/inference.html"
+glue::glue(
+  "\nFurther explanation regarding interpretation",
+  " and methodology can be found in the [documentation of `touchstone`]({link})." # nolint
+)

touchstone/header.R

@@ -0,0 +1,13 @@
+# You can modify the PR comment header here. You can use github markdown e.g.
+# emojis like :tada:.
+# This file will be parsed and evaluate within the context of
+# `benchmark_analyze` and should return the comment text as the last value.
+# Available variables for glue substitution:
+# * ci: confidence interval
+# * branches: BASE and HEAD branches benchmarked against each other.
+# See `?touchstone::pr_comment`
+glue::glue(
+  "This is how benchmark results would change (along with a",
+  " {100 * ci}% confidence interval in relative change) if ",
+  "{system2('git', c('rev-parse', 'HEAD'), stdout = TRUE)} is merged into {branches[1]}:\n" # nolint
+)