fix: model plot and pred parsing

.Rbuildignore

@@ -4,7 +4,6 @@
 ^other$g
 ^.*\.Rproj$
 ^\.Rproj\.user$
-compile.*
 .vscode
 ^_pkgdown\.yml$
 ^docs$
@@ -15,5 +14,32 @@ compile.*
 .nojekyll
 .gitkeep
 ^man-roxygen
-^README\.Rmd$
+^README\.qmd$
+^README_files/
 logo.png
+^vignettes/articles$
+^vignettes/.quarto
+^Archived/
+^src/\.cargo$
+^src/rust/target/
+^.*_test\.R$
+^.*_old.R$
+rust_debug.txt
+^inst/template/
+^get-dependencies
+^target/
+^inst/Learn/.quarto
+^inst/Learn/_*
+Experimental
+
+
+^\.vscode$
+^src/rust/vendor$
+^src/rust/target$
+^src/Makevars$
+^src/Makevars\.win$
+
+^Cargo\.toml$
+^Cargo\.lock$
+
+^Images/

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,25 @@
+---
+name: Bug report
+about: Report bugs and issues with the package
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Version information**
+ - OS: [e.g. MacOS, Windows, Linux]
+ - R:   
+
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Feature request: '
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/build.yml

@@ -0,0 +1,43 @@
+name: R Package Check
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::roxygen2
+          needs: check
+
+      - name: Verify roxygen outputs are current
+        run: |
+          Rscript -e 'roxygen2::roxygenise()'
+          git status --short man NAMESPACE inst/NEWS.Rd || true
+          git diff --quiet man NAMESPACE inst/NEWS.Rd || (echo "::error::Run devtools::document() and commit regenerated Rd/NAMESPACE files." && exit 1)
+
+      - name: Check package
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -32,16 +33,16 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, any::rsconnect, local::.
+          extra-packages: any::pkgdown, local::.
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, quiet = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.gitignore

@@ -1,32 +1,80 @@
-.Rproj.user
+# R session & IDE noise
 .Rhistory
+.Rapp.history
 .RData
+.RDataTmp
 .Ruserdata
+.Renviron
+.Rproj.user/
+.vscode/
 .DS_Store
+PmetricsGit.Rproj
+
+# Build/check artifacts
+/*.tar.gz
+/*.Rcheck/
+..Rcheck/
 Pmetrics.Rcheck/
-#build
-Archived
+*_cache/
+/cache/
+*.utf8.md
+*.knit.md
+.Rd2pdf*/
+rsconnect/
+po/*~
+
+# Vignettes/docs rendered locally
+vignettes/*.html
+vignettes/*.pdf
+vignettes/*_files/
+inst/doc/
 PACKAGES.gz
 PACKAGES.rds
 PMchangelog.html
+
+# Credentials/tokens
+.httr-oauth
+
+# Compiled objects
+src/*.o
+src/*.so
+src/*.dll
 src/Pmetrics.so
 src/knn.o
 src/registerDynamicSymbol.o
-src/Pmetrics.dll
-PmetricsGit.Rproj
-inst/compiledFortran/
-.DS_Store
 src/symbols.rds
+inst/compiledFortran/
+
+# Rust artifacts
+target/
+Cargo.lock
+
+# Generated config/templates
+inst/rust/template/*
+
+# Training book outputs
+inst/Learn/.quarto/
+inst/Learn/_book/
+inst/Learn/_site/
+inst/Learn/_freeze/
+
+# Simulation / report artifacts
+data-raw/Runs/
 tests/testthat/Runs/
-..Rcheck/
-.vscode/
-.Rd2pdf65996/
-other/
-.Rprofile
 Examples
-.Rdata
-.httr-oauth
-inst/rust/template/*
-inst/options/PMoptions.json
-inst/options/PMoptions.json
-inst/doc
+Experimental
+other/
+1
+2
+3
+
+# Misc project outputs
+*_test.R
+docs/
+docs
+src/rust/vendor
+src/Makevars
+src/Makevars.win
+
+/.quarto/
+**/*.quarto_ipynb

Archived/.gitignore

@@ -0,0 +1 @@
+PmetricsManual