update

.github/workflows/Render-Book.yaml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: ubuntu-20.04, r: '4.1.0'}
+          - {os: ubuntu-20.04, r: '4.1.1'}
           # - {os: macos-11, r: '4.1.0'}
 
     env:

DESCRIPTION

@@ -10,6 +10,7 @@ Imports:
   arules (>= 1.6-8),
   autoplotly (>= 0.1.4),
   bayesplot (>= 1.8.1),
+  bbmle (>= 1.0.24),
   beanplot (>= 1.2),
   BiocManager (>= 1.30.16),
   bookdown (>= 0.22),
@@ -53,11 +54,11 @@ Imports:
   heatmaply (>= 1.2.1),
   highcharter (>= 0.8.2),
   hrbrthemes (>= 0.8.0),
-  INLA (>= 21.02.23),
   knitr (>= 1.33),
   kableExtra (>= 1.3.4),
   Kendall (>= 2.2),
   leaflet (>= 2.0.4.1),
+  leafletCN (>= 0.2.1),
   lightgbm (>= 3.2.0),
   lme4 (>= 1.1-27.1),
   magick (>= 2.7.2),
@@ -104,6 +105,7 @@ Imports:
   sp (>= 1.4-2),
   sparkline (>= 2.0),
   spDataLarge (>= 0.5.4),
+  splines2 (>= 0.4.3),
   sparklyr (>= 1.7.1),
   StanHeaders (>= 2.26.2),
   SuppDists (>= 1.1-9.5),

_bookdown.yml

@@ -15,36 +15,47 @@ before_chapter_script: ["_common.R"]
 rmd_files:
 - "index.Rmd"
 
-- "preface.Rmd"   # 前言
-- "notations.Rmd" # 符号表
+- "preface.Rmd"                # 前言
 
-# R 语言
-
-- "file-operations.Rmd"      # 文件操作
-- "data-structure.Rmd"       # R 语言数据结构
-- "data-manipulation.Rmd"    # 数据操作
 
+# 数据处理
+- "data-wrangling.Rmd"
+- "data-structure.Rmd"         # R 语言数据结构
 - "data-transportation.Rmd"    # 数据导入导出
-- "graphics-foundations.Rmd"   # 图形基础
-- "data-visualization.Rmd"     # 数据可视化
-- "dynamic-documents.Rmd"      # 动态文档
-
+- "string-operations.Rmd"      # 字符串操作
+- "regular-expressions.Rmd"    # 正则表达式
+- "data-manipulation.Rmd"      # 数据操作
+
+# 统计图形
+- "statistical-graphics.Rmd"
+- "graphics-foundations.Rmd"           # 图形基础
+- "data-visualization.Rmd"             # 数据可视化
 - "interactive-web-graphics.Rmd"       # 交互式网页图形
+
+# 文档
+- "dynamic-documents.Rmd"              # 动态文档
+- "document-elements.Rmd"              # 文档元素
+- "portable-documents.Rmd"             # 便携式文档
+- "web-documents.Rmd"                  # 网页文档
+- "office-documents.Rmd"               # 办公文档
+- "reproducible-workflows.Rmd"         # 可重复性工作流
+- "advanced-documents.Rmd"             # 大型应用
+
+# 数据产品
+- "data-product.Rmd"
 - "interactive-data-tables.Rmd"        # 交互式表格
 - "interactive-shiny-app.Rmd"          # 交互式仪表盘
 
-- "string-operations.Rmd"    # 字符串操作
-- "regular-expressions.Rmd"  # 正则表达式
-- "text-analysis.Rmd"        # 文本分析
-
-# 现代统计
-
+# 统计基础
+- "statistical-foundations.Rmd"
 - "sampling-distributions.Rmd"   # 抽样分布
 - "parameter-estimators.Rmd"     # 参数估计
 - "hypothesis-test.Rmd"          # 假设检验
 - "power-analysis.Rmd"           # 功效分析
 - "experimental-design.Rmd"      # 试验设计
 
+# 统计模型
+- "statistical-models.Rmd"
 - "linear-models.Rmd"                  # 线性模型
 - "generalized-linear-models.Rmd"      # 广义线性模型
 #- "generalized-additive-models.Rmd"   # 广义可加模型
@@ -54,18 +65,27 @@ rmd_files:
 #- "generalized-linear-mixed-effects-models.Rmd" # 广义线性混合效应模型
 #- "generalized-additive-mixed-models.Rmd"       # 广义可加混合效应模型
 #- "nonlinear-mixed-models.Rmd"                  # 非线性混合效应模型
+- "bayesian-models.Rmd"         # 贝叶斯模型
 
-- "case-study.Rmd"              # 案例学习
-- "data-explorer.Rmd"           # 数据探索
+# 数据建模
+- "data-modeling.Rmd"
+- "text-analysis.Rmd"           # 文本分析
 - "survival-analysis.Rmd"       # 生存分析
 - "time-series-analysis.Rmd"    # 时序分析
+
+# 时空统计
+- "spatio-temporal-data.Rmd"
 - "spatial-analysis.Rmd"        # 空间分析
 - "spatial-modeling.Rmd"        # 空间建模
+- "spatial-viz.Rmd"
+
+# 统计应用
+- "case-study.Rmd"              # 案例学习
+- "data-explorer.Rmd"           # 数据探索
 
-- "bayesian-models.Rmd"         # 贝叶斯模型
 
 # 机器学习
-#- "machine-learning.Rmd"
+- "machine-learning.Rmd"
 
 #- "k-means-clustering.Rmd"
 #- "k-nearest-neighbors.Rmd"
@@ -76,24 +96,27 @@ rmd_files:
 #- "decision-trees.Rmd"
 #- "random-forests.Rmd"
 - "gradient-boosting-machine.Rmd"
-- "neural-networks.Rmd"
+# - "neural-networks.Rmd"
 
-- "matrix-operations.Rmd" # 矩阵运算
-- "symbolic-computation.Rmd"
-- "numerical-optimization.Rmd" # 数值优化
+# 运筹优化
+
+- "numerical-optimization.Rmd"               # 数值优化
 #- "expectation-maximization.Rmd"
 #- "markov-chain-monte-carlo.Rmd"
 
 #- "deep-learning.Rmd"
-#- "natural-language-processing.Rmd" # 文本挖掘 分词 主题模型 LDA
+#- "natural-language-processing.Rmd"         # 文本挖掘 分词 主题模型 LDA
 
-- "appendix.Rmd"        # 附录和命令行操作
-- "other-softwares.Rmd" # 其它软件工具
+- "appendix.Rmd"                    # 附录和命令行操作
+- "matrix-operations.Rmd"           # 矩阵运算
+- "symbolic-computation.Rmd"
 
-- "mixed-programming.Rmd"           # R 和其它语言的混合编程
+- "mixed-programming.Rmd"           # 混合编程
 - "object-oriented-programming.Rmd" # 面向对象编程
-
+- "file-operations.Rmd"             # 文件操作
+- "other-softwares.Rmd"             # 其它软件工具
 #- "random-vector.Rmd"
 #- "stochastic-process.Rmd"
+- "notations.Rmd"                   # 符号表
 
 - "references.Rmd"

_common.R

@@ -1,16 +1,18 @@
-knitr::opts_chunk$set(width = 69, dpi = 300, message = FALSE, fig.align='center')
+knitr::opts_chunk$set(width = 69, dpi = 300, message = FALSE, fig.align = "center")
 
 # convert pdf to png
 to_png <- function(fig_path) {
   png_path <- sub("\\.pdf$", ".png", fig_path)
-  magick::image_write(magick::image_read_pdf(fig_path), format = "png", path = png_path,
-                      density = 300, quality = 100)
+  magick::image_write(magick::image_read_pdf(fig_path),
+    format = "png", path = png_path,
+    density = 300, quality = 100
+  )
   return(png_path)
 }
 
 # embed math fonts to pdf
 embed_math_fonts <- function(fig_path) {
-  if(knitr::is_latex_output()){
+  if (knitr::is_latex_output()) {
     embedFonts(
       file = fig_path, outfile = fig_path,
       fontpaths = system.file("fonts", package = "fontcm")
@@ -21,15 +23,15 @@ embed_math_fonts <- function(fig_path) {
 
 knitr::knit_hooks$set(output = local({
   # the default output hook
-  hook_output = knitr::knit_hooks$get('output')
+  hook_output <- knitr::knit_hooks$get("output")
   function(x, options) {
     if (!is.null(n <- options$out.lines)) { # out.lines
-      x = xfun::split_lines(x)
+      x <- xfun::split_lines(x)
       if (length(x) > n) {
         # truncate the output
-        x = c(head(x, n), '....\n')
+        x <- c(head(x, n), "....\n")
       }
-      x = paste(x, collapse = '\n') # paste first n lines together
+      x <- paste(x, collapse = "\n") # paste first n lines together
     }
     hook_output(x, options)
   }
@@ -41,15 +43,15 @@ palette(c(
   "#4285f4", # GoogleBlue
   "#34A853", # GoogleGreen
   "#FBBC05", # GoogleYellow
-  "#EA4335"  # GoogleRed
+  "#EA4335" # GoogleRed
 ))
 
 is_on_travis <- identical(Sys.getenv("TRAVIS"), "true")
 is_online <- curl::has_internet()
 is_latex <- identical(knitr::opts_knit$get("rmarkdown.pandoc.to"), "latex")
 is_html <- identical(knitr::opts_knit$get("rmarkdown.pandoc.to"), "html")
-is_windows <- identical(.Platform$OS.type, 'windows')
-is_unix <- identical(.Platform$OS.type, 'unix')
+is_windows <- identical(.Platform$OS.type, "windows")
+is_unix <- identical(.Platform$OS.type, "unix")
 
 # 创建临时的目录存放数据集
-if(!dir.exists(paths = "./data")) dir.create(path = "./data")
+if (!dir.exists(paths = "./data")) dir.create(path = "./data")

advanced-documents.Rmd

@@ -0,0 +1,14 @@
+# 高级文档 {#chap-advanced-documents}
+
+## 编写书籍 {#sec-bookdown}
+
+此外， [ElegantTufteBookdown](https://github.com/XiangyunHuang/ElegantTufteBookdown) 项目提供了 tufte 风格的书籍模板，本书配套的仓库目录 `examples/` 下准备了一系列常用模板。
+
+## 个人网站 {#sec-blogdown}
+
+## R 包文档 {#sec-pkgdown}
+
+## 课程网站 {#sec-rmarkdown}
+
+
+

book.bib

@@ -137,7 +137,22 @@ @Inbook{Deb2005
   doi      = "10.1007/0-387-28356-0_10",
   url      = "https://doi.org/10.1007/0-387-28356-0_10"
 }
-
+@Article{Ryacas,
+  title = {{Ryacas: A computer algebra system in R}},
+  author = {Mikkel Meyer Andersen and Søren Højsgaard},
+  journal = {Journal of Open Source Software},
+  year = {2019},
+  volume = {4},
+  number = {42},
+  url = {https://doi.org/10.21105/joss.01763},
+}
+@Article{mgcViz,
+  author = {Matteo Fasiolo and Raphael Nedellec and Yannig Goude and Simon N. Wood},
+  title = {Scalable visualisation methods for modern Generalized Additive Models.},
+  journal = {Arxiv preprint},
+  year = {2018},
+  url = {https://arxiv.org/abs/1809.10632},
+}
 @Article{heatmaply2017,
     author = {{Galili} and {Tal} and {O'Callaghan} and {Alan} and {Sidi} and {Jonathan} and {Sievert} and {Carson}},
     title = {{heatmaply}: an R package for creating interactive cluster heatmaps for online publishing},
@@ -1839,3 +1854,14 @@ @article{RS_2020_John
   volume = {12},
   number = {1}
 }
+
+@Article{Pebesma_2005_sp,
+  author = {Edzer J. Pebesma and Roger S. Bivand},
+  title = {Classes and methods for spatial data in {R}},
+  journal = {R News},
+  year = {2005},
+  volume = {5},
+  number = {2},
+  pages = {9--13},
+  url = {https://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf},
+}

dashboard/007-shiny-app/README.md

@@ -1,23 +1,5 @@
-Old Faithful Geyser Data
-美国怀俄明州黄石国家公园-老忠实间歇泉
-每隔一段时间就喷发，非常守时规律，表现得很老实，故而得名
+### Old Faithful Geyser Data 
 
-维基百科的介绍
-https://en.wikipedia.org/wiki/Old_Faithful
-用这个数据集讲一个故事
-
-数据集介绍
-https://stat.ethz.ch/R-manual/R-patched/library/datasets/html/faithful.html
-
-更大范围的数据集
-http://www.stat.yale.edu/~jah49/Pictures_in_R/Fickle_Old_Faithful/OldFaithful.pdf
-
-如果只想获得数据集可以从这下载
-https://www.stat.cmu.edu/~larry/all-of-statistics/=data/faithful.dat
-
-MASS 的 geyser 数据集（299 条记录）比 Base R 自带的 faithful 数据集（272 条记录）多 27 条数据
-
-把窗宽的概念、二维核密度估计的概念
-
-一维的密度、直方图
+美国怀俄明州黄石国家公园-老忠实间歇泉，每隔一段时间就喷发，非常守时规律，表现得很老实，故而得名。
 
+https://en.wikipedia.org/wiki/Old_Faithful

data-modeling.Rmd

@@ -0,0 +1,5 @@
+# (PART) 数据建模 {-}
+
+# 介绍 {#chap-data-modeling .unnumbered}
+
+数据建模

data-product.Rmd

@@ -0,0 +1,5 @@
+# (PART) 数据产品 {-}
+
+# 介绍 {#chap-data-product .unnumbered}
+
+数据产品