Docs

.gitattributes

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+*.pdf binary
+*.png binary
+*.xlsx binary

.github/pull_request_template.md

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+## Summary
+
+Describe the tutorial change and why it is needed.
+
+## Affected content
+
+- [ ] Package overview or setup
+- [ ] Module 1: `Stat`
+- [ ] Module 2: `Train_Model`
+- [ ] Module 3: `Subtyping`
+- [ ] Module 4: `PrognosiX`
+- [ ] Data, figures, or GitHub workflow
+
+## Validation
+
+- [ ] `quarto inspect` succeeds
+- [ ] `quarto render` succeeds, or the reason it was not run is documented
+- [ ] Important figures appear below their generating chunks
+- [ ] New or changed figures have captions or alternative text
+- [ ] No generated HTML, caches, or temporary analysis output is committed
+- [ ] Numerical or scientific changes are described below
+
+## Scientific output changes
+
+List any changed results, figures, dependencies, or interpretation. Write “None” when the change affects prose only.

.github/workflows/quarto-pages.yml

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+name: Render and deploy the Quarto book
+
+on:
+  push:
+    branches: [docs]
+  pull_request:
+    branches: [docs]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the book source
+        uses: actions/checkout@v5
+
+      - name: Check out the icare package source
+        uses: actions/checkout@v5
+        with:
+          repository: YuLab-SMU/icare
+          ref: main
+          path: .ci/icare
+
+      - name: Check out the archived DMwR source
+        uses: actions/checkout@v5
+        with:
+          repository: cran/DMwR
+          path: .ci/DMwR
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install icare and its workflow dependencies
+        shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ github.token }}
+        run: |
+         install.packages(c(
+           "remotes",
+           "BiocManager",
+
+           # Classification / caret backends
+           "caret",
+           "caretEnsemble",
+           "randomForest",
+           "glmnet",
+           "gbm",
+           "rpart",
+           "klaR",
+           "C50",
+           "ranger",
+
+           # icare Suggests available from CRAN
+           "Boruta",
+           "DALEX",
+           "DT",
+           "Hmisc",
+           "NMF",
+           "NbClust",
+           "RANN",
+           "ROSE",
+           "Rtsne",
+           "UpSetR",
+           "autoReg",
+           "bbotk",
+           "bslib",
+           "c060",
+           "dcurves",
+           "digest",
+           "e1071",
+           "factoextra",
+           "flextable",
+           "forestploter",
+           "ipred",
+           "jsonlite",
+           "magrittr",
+           "maxstat",
+           "mclust",
+           "mice",
+           "mlbench",
+           "mlr3",
+           "mlr3learners",
+           "mlr3mbo",
+           "mlr3pipelines",
+           "mlr3tuning",
+           "mlr3viz",
+           "nnls",
+           "nricens",
+           "officer",
+           "paradox",
+           "plotly",
+           "rBayesianOptimization",
+           "randomForestSRC",
+           "risksetROC",
+           "rms",
+           "shapviz",
+           "shiny",
+           "shinydashboard",
+           "survex",
+           "survminer",
+           "testthat",
+           "themis",
+           "tidyverse",
+           "timeROC",
+           "umap"
+           )) 
+
+          remotes::install_github(
+            c(
+            "mlr-org/mlr3extralearners",
+            "mlr-org/mlr3proba",
+            "mlr-org/mlr3tuningspaces"
+            ),
+            upgrade = "never",
+            dependencies = TRUE
+          )
+
+          BiocManager::install(c("ComplexHeatmap","survcomp","Biobase"), ask = FALSE, update = FALSE)
+
+          remotes::install_local(
+            ".ci/DMwR",
+            dependencies = TRUE,
+            upgrade = "never"
+          )
+          remotes::install_local(
+            ".ci/icare",
+            dependencies = TRUE,
+            upgrade = "never"
+          )
+
+      - name: Render the book
+        run: quarto render
+
+      - name: Upload the Pages artifact
+        if: github.event_name != 'pull_request'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _book
+
+  deploy:
+    if: github.event_name != 'pull_request'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

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-.trae
-PrognosiX
-local-test/
-StatObject/
+.DS_Store
+.Rhistory
+.RData
+.Rproj.user/
+.quarto/
+.ci/
+_book/
+_freeze/
+*_cache/
+*_files/
+*.knit.md
+*.utf8.md
+
+# Objects and chapter output generated during execution
+*.rds
+Figures/
+Module*_Output/
+PrognosiX*_Output/
+NRIDI_Manual_Results/

CONTRIBUTING.md

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+# Contributing to the icare tutorial
+
+Changes to this book are reviewed through GitHub pull requests targeting the `docs` branch.
+
+## Before opening a pull request
+
+- Keep prose and code in English.
+- Use small R chunks with a unique `#| label:` and place an explanation immediately before the chunk.
+- Let important plots display directly below the chunk that creates them.
+- Do not commit `_book/`, Quarto caches, frozen execution output, temporary R objects, or analysis output directories.
+- Preserve a strict development/validation boundary in modeling examples.
+- Do not change a package function name or claimed capability without checking the current `main` branch of `YuLab-SMU/icare`.
+- Add new static manuscript figures under the matching `image/module*/` directory and prefer vector PDF output.
+- Use informative alternative text or a clear figure caption for every reader-facing figure.
+
+## Validation
+
+Run the structural check:
+
+```bash
+quarto inspect
+```
+
+When the required R packages and data are available, run a full render:
+
+```bash
+quarto render
+```
+
+Review the GitHub Actions result before merging. A pull request should explain the affected chapter, any changed output, new dependencies, and whether numerical results or figures were regenerated.
+
+## Scope
+
+Tutorial-only changes belong in this branch. Changes to the R package, exported API, package documentation, or bundled R data should be proposed against the package's `main` branch instead.