将贝叶斯建模、机器学习和空间分析拆分到《现代应用统计》

.github/workflows/quarto-book-macos.yaml

@@ -11,7 +11,6 @@ jobs:
     runs-on: macos-14
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CMDSTAN_VERSION: "2.34.1"
       PANDOC_VERSION: "3.1.11"
       RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow
     steps:
@@ -26,7 +25,7 @@ jobs:
         with:
           use-public-rspm: true
           r-version: '4.3.2'
-          extra-repositories: 'https://mc-stan.org/r-packages https://inla.r-inla-download.org/R/stable https://grantmcdermott.r-universe.dev'
+          extra-repositories: 'https://grantmcdermott.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
 
@@ -41,15 +40,6 @@ jobs:
           # install full prebuilt version
           TINYTEX_INSTALLER: TinyTeX
 
-      - name: Setup CmdStan
-        run: |
-          curl -fLo cmdstan-${CMDSTAN_VERSION}.tar.gz https://github.com/stan-dev/cmdstan/releases/download/v${CMDSTAN_VERSION}/cmdstan-${CMDSTAN_VERSION}.tar.gz
-          sudo mkdir -p /opt/cmdstan/
-          sudo chown -R $(whoami):staff /opt/cmdstan/
-          tar -xzf cmdstan-${CMDSTAN_VERSION}.tar.gz -C /opt/cmdstan/
-          make build -C /opt/cmdstan/cmdstan-${CMDSTAN_VERSION}
-          rm cmdstan-${CMDSTAN_VERSION}.tar.gz
-
       - name: Install Fonts From System
         run: |
           export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
@@ -93,7 +83,6 @@ jobs:
         env:
           RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow
           RETICULATE_PYTHON: /opt/.virtualenvs/r-tensorflow/bin/python
-          CMDSTAN: /opt/cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}
 
       - name: Deploy book to bookdown.org
         if: github.event_name == 'push'

.github/workflows/quarto-book-ubuntu.yaml

@@ -11,7 +11,6 @@ jobs:
     runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CMDSTAN_VERSION: "2.34.1"
       PANDOC_VERSION: "3.1.11"
       RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow
     steps:
@@ -26,7 +25,7 @@ jobs:
         with:
           use-public-rspm: true
           r-version: '4.3.2'
-          extra-repositories: 'https://mc-stan.org/r-packages https://inla.r-inla-download.org/R/stable https://grantmcdermott.r-universe.dev'
+          extra-repositories: 'https://grantmcdermott.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
 
@@ -52,14 +51,6 @@ jobs:
           python -m spacy download zh_core_web_sm
           deactivate
 
-      - name: Setup CmdStan
-        run: |
-          curl -fLo cmdstan-${CMDSTAN_VERSION}.tar.gz https://github.com/stan-dev/cmdstan/releases/download/v${CMDSTAN_VERSION}/cmdstan-${CMDSTAN_VERSION}.tar.gz
-          mkdir -p /opt/cmdstan/
-          tar -xzf cmdstan-${CMDSTAN_VERSION}.tar.gz -C /opt/cmdstan/
-          make build -C /opt/cmdstan/cmdstan-${CMDSTAN_VERSION}
-          rm cmdstan-${CMDSTAN_VERSION}.tar.gz
-
       - name: Install Fonts From System
         run: |
           sudo apt-get install -y ghostscript graphviz optipng
@@ -96,7 +87,6 @@ jobs:
         env:
           RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow
           RETICULATE_PYTHON: /opt/.virtualenvs/r-tensorflow/bin/python
-          CMDSTAN: /opt/cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}
 
       - name: Deploy to Github Pages
         uses: JamesIves/github-pages-deploy-action@v4

.gitignore

@@ -18,22 +18,7 @@ _book/
 rsconnect/
 site_libs/
 data-raw/
-code/poisson_log_glm
-code/bernoulli_logit_glm_normal
-code/bernoulli_logit_glm_lasso
-code/bernoulli_logit_glm_horseshoe
-code/gaussian_process_simu
-code/gaussian_process_fitted
-code/gaussian_process_pred
-code/multi_normal_simu
-code/multi_normal_fitted
-code/rongelap_poisson_pred
-code/rongelap_poisson_processes
-code/faithful_finite_mixtures
-code/faithful_2d_finite_mixtures
-code/eight_schools
-code/rats
-code/stochastic_volatility_models
+
 *.log
 *-tikzDictionary
 *.aux

DESCRIPTION

@@ -10,16 +10,10 @@ BugReports: https://github.com/XiangyunHuang/data-analysis-in-action/issues
 Depends: 
     R (>= 4.3.0)
 Imports:
-    abess,
-    bayesplot,
     BB,
     beanplot,
-    BH,
-    blme,
-    brms,
     broom,
     car,
-    cmdstanr (>= 0.7.1),
     coin,
     data.table,
     datasauRus,
@@ -31,15 +25,8 @@ Imports:
     dygraphs,
     e1071,
     ECOSolveR,
-    expm,
-    fastmatrix,
-    fGarch (>= 4031.90),
-    fmesher,
-    FRK (>= 2.2.0),
-    keras,
     kernlab,
     GA (>= 3.2.3),
-    geodata (>= 0.4.13),
     gifski,
     ggalluvial,
     gganimate (>= 1.0.9),
@@ -63,81 +50,52 @@ Imports:
     ggTimeSeries,
     ggVennDiagram,
     ggwordcloud,
-    glmmTMB,
-    glmnet,
-    GLMMadaptive,
     gt (>= 0.10.1),
     hexbin,
     HistData,
-    hglm,
-    INLA (>= 23.9.9),
     jiebaR,
     knitr (>= 1.44),
-    lars,
     latticeExtra,
-    lavaan,
-    lme4,
-    loo (>= 2.6.0),
     lvplot (>= 0.2.1),
     magick,
     maps,
-    MCMCglmm,
     misc3d,
-    ncvreg,
     nloptr,
     nomnoml (>= 0.3.0),
     patchwork,
     pdftools,
     plot3D,
     plotly (>= 4.10.1),
-    pls,
     pROC,
-    projpred,
     pwr,
     purrr (>= 1.0.0),
     quadprog,
     quantmod,
     ragg,
-    randomForest,
-    reticulate,
-    rjags,
     ROI,
     ROI.plugin.ecos,
     ROI.plugin.glpk,
     ROI.plugin.nloptr,
     ROI.plugin.quadprog,
     ROI.plugin.scs,
     rootSolve,
-    rpart.plot,
     RSQLite,
-    rstan (>= 2.32.3),
     scs,
-    sf (>= 1.0.9),
     showtext,
     spacyr,
-    spaMM,
-    spdep,
-    splancs,
-    spatstat,
-    stars (>= 0.6.0),
-    tensorflow,
     text2vec,
-    tidycensus,
     tidygraph,
     tinyplot,
     titanic,
     tikzDevice,
     treemapify,
     TSP,
     vcd,
-    VGAM,
     vioplot,
     visNetwork,
     webshot2,
-    xgboost,
     xml2,
     xts
-LinkingTo: StanHeaders (>= 2.32.2), RcppParallel (>= 5.1.0)
 Remotes:
     davidsjoberg/ggbump,
     davidsjoberg/ggstream
@@ -148,8 +106,6 @@ Enhances:
     sp (>= 2.0-0)
 SystemRequirements: pgf (>= 3.00), JAGS 4.x.y
 Additional_repositories:
-    https://mc-stan.org/r-packages/,
-    https://grantmcdermott.r-universe.dev,
-    https://inla.r-inla-download.org/R/stable
+    https://grantmcdermott.r-universe.dev
 Encoding: UTF-8
 License: CC NC ND 4.0

README.md

@@ -24,24 +24,11 @@
 -   数据建模
     -   网络分析（R 语言社区开发者协作网络）
     -   时序分析（美团股价收益率的风险建模）
-    -   空间分析（预测核辐射强度的空间分布）
 -   优化建模
     -   统计计算（统计模型与优化问题的关系）
     -   数值优化（线性、非线性、约束和无约束）
     -   优化问题（TSP 问题、投资组合问题等）
--   贝叶斯建模
-    -   概率推理框架
-    -   广义线性模型
-    -   分层正态模型
-    -   混合效应模型
-    -   广义可加模型
-    -   高斯过程回归
--   机器学习
-    -   分类问题
-    -   回归问题
 -   附录
-    -   数学符号
-    -   矩阵运算
     -   Git 和 Github
 
 ## 在线编译网页书籍

_quarto.yml

@@ -64,34 +64,13 @@ book:
         - analyze-text-data.qmd
         - analyze-survival-data.qmd
         - analyze-time-series-data.qmd
-    - part: "空间分析"
-      chapters:
-        - analyze-point-pattern.qmd
-        - analyze-spatial-data.qmd
-        - analyze-areal-data.qmd
     - part: "优化建模"
       chapters:
         - statistical-computation.qmd
         - numerical-optimization.qmd
         - optimization-problems.qmd
-    - part: "贝叶斯建模"
-      chapters:
-        - probabilistic-reasoning-framework.qmd
-        - generalized-linear-models.qmd
-        - hierarchical-normal-models.qmd
-        - mixed-effects-models.qmd
-        - generalized-additive-models.qmd
-        - gaussian-processes-regression.qmd
-        - time-series-regression.qmd
-    - part: "机器学习"
-      chapters:
-        - classification-problems.qmd
-        - clustering-problems.qmd
-        - regression-problems.qmd
     - references.qmd
   appendices:
-    - notations.qmd
-    - matrix-operations.qmd
     - git-github.qmd
   repo-branch: main
   search: true