merge main

SD/20240321_0_R实践课程/index.qmd

@@ -1,153 +0,0 @@
----
-title: "〇、R语言实践前篇"
-subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
-author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
-date: today
-lang: zh
-format:
-  revealjs:
-    theme: dark
-    slide-number: true
-    chalkboard:
-      buttons: true
-    preview-links: auto
-    lang: zh
-    toc: true
-    toc-depth: 1
-    toc-title: 大纲
-    logo: ./_extensions/inst/img/ucaslogo.png
-    css: ./_extensions/inst/css/revealjs.css
-    pointer:
-      key: "p"
-      color: "#32cd32"
-      pointerSize: 18
-revealjs-plugins:
-  - pointer
-filters:
-  - d2
----
-
-```{r}
-#| include: false
-#| cache: false
-lang <- "cn"
-require(tidyverse)
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-## R语言实践部分课程简介
- 
-**接下来的课程由我来带着大家一起学习、实践基于R语言的数据分析。**
-
-### 自我介绍
-
-- 苏命：来自中国科学院生态环境研究中心
-- 主要从事**水源水质水生态**方面的研究
-
-### 课件
-
-- 采用`R语言`+`quarto`完成
-- 网页公开：[https://drwater.rcees.ac.cn/course/public/RWEP/\@PUB/index.html](https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/index.html)
-- 课件代码：[https://drwater.rcees.ac.cn/git/course/RWEP.git](https://drwater.rcees.ac.cn/git/course/RWEP.git)
-- 代码web界面： [https://on.tty-share.com/s/hWkn5_eF6rfZuAyJu8sheMgrcRzx6AZ2m7V32IphFHs7gn-vP9WYOeVEYtH8a-bGTuM/](https://on.tty-share.com/s/hWkn5_eF6rfZuAyJu8sheMgrcRzx6AZ2m7V32IphFHs7gn-vP9WYOeVEYtH8a-bGTuM/)
-
-## 如何学习接下来的内容？
-
-- 上课形式：
-  - **实践操作为主**，目的是让每一位同学都能独立开展基于R的数据分析
-  - **2-3人一组**，自由分组，相互帮助
-- 准备工作：
-  - 个人笔记本电脑，Microsoft Windows、GNU/Linux、MacOS系统
-  - 安装好**Microsoft Excel**
-  - 能联网
-  - 如果电池不够用，建议带上插座
-- 上课规则
-  - 可随时打断，**不懂就问**
-  - **无特殊情况不迟到**，否则操作过程容易跟不上
-
-## Rstudio Server使用
-
-- 服务网址：[https://drwater.rcees.ac.cn/rs1/](https://drwater.rcees.ac.cn/rs1/)
-- 每位同学使用1个账号，随机生成
-- 密码：****
-- 后面的实践课程可在该服务器上完成
-
-
-## 请记住自己的账号！
-
-::: {layout-ncol=2}
-
-```{r}
-#| echo: false
-#| output: asis
-coursememberdf <- readxl::read_xlsx("../../data/course_member.xlsx")
-nmem <- nrow(coursememberdf)
-set.seed <- 23
-
-uiddf <- coursememberdf |>
-  dplyr::mutate(uid = paste0("ruser", sprintf("%02d", sample(1:nmem, nmem)))) |>
-  dplyr::select(uid, 姓名) |>
-  dplyr::mutate(姓名 = "**") |>
-  dplyr::arrange(uid) |>
-  dplyr::mutate(group = (dplyr::row_number() - 1) %/% 10 + 1) |>
-  tidyr::nest(gdf = -group) |>
-  dplyr::mutate(tab = purrr::map(gdf, ~ knitr::kable(.x)))
-
-uiddf$tab[[1]]
-uiddf$tab[[2]]
-
-```
-:::
-
-## 请记住自己的账号！
-
-::: {layout-ncol=2}
-
-```{r}
-#| echo: false
-#| output: asis
-
-uiddf$tab[[3]]
-uiddf$tab[[4]]
-```
-:::
-
-## 课后作业
-
-提交形式：`第*次作业_姓名.qmd`文件
-
-模板：
-
-````
----
-title: "课后作业*"
-author: 姓名
----
-
-
-# 第1题
-
-说明
-
-```{r}
-# Here is the code
-
-```
-
-# 第2题
-
-说明
-
-```{r}
-# Here is the code
-
-```
-
-````
-
-
-## 欢迎讨论！{.center}
-
-
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
-

SD/20240321_1_R语言介绍/index.qmd

@@ -218,4 +218,4 @@ devtools::install_github("kjhealy/socviz")
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240321_2_R语言语法基础/index.qmd

@@ -792,4 +792,4 @@ names(Y) <- c("colA", "colB", "colC")
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240321_3_Excel基础/index.qmd

@@ -130,4 +130,4 @@ require(learnr)
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240326_1_codestyle/_extensions

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+../../_extensions

SD/20240326_1_codestyle/index.qmd

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+---
+title: "代码编写规则"
+subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
+author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
+date: today
+lang: zh
+format:
+  revealjs:
+    theme: dark
+    slide-number: true
+    chalkboard:
+      buttons: true
+    preview-links: auto
+    lang: zh
+    toc: true
+    toc-depth: 1
+    toc-title: 大纲
+    logo: ./_extensions/inst/img/ucaslogo.png
+    css: ./_extensions/inst/css/revealjs.css
+    pointer:
+      key: "p"
+      color: "#32cd32"
+      pointerSize: 18
+revealjs-plugins:
+  - pointer
+filters:
+  - d2
+---
+
+
+```{r}
+#| echo: false
+knitr::opts_chunk$set(echo = TRUE)
+# source("../../coding/_common.R")
+library(tidyverse)
+library(nycflights13)
+```
+
+
+## tidy data
+
+```{r}
+knitr::include_graphics("../../image/tidy-1.png", dpi = 270)
+```
+
+
+## pipe（管道） |>
+
+```{r}
+#| eval: false
+require(patchwork)
+plot(1:10)
+1:10 |> plot()
+plot(x = 1:10, y = sin(1:10))
+1:10 |> plot(y = sin(1:10))
+
+```
+
+```{r}
+#| echo: false
+#| layout-nrow: 1
+#| fig-width: 4
+#| fig-height: 3
+#| out-height: 90%
+require(patchwork)
+plot(1:10)
+1:10 |> plot()
+plot(x = 1:10, y = sin(1:10))
+1:10 |> plot(y = sin(1:10))
+
+```
+
+
+
+## pipe（管道）：%>%
+
+```{r}
+#| eval: false
+#| layout-nrow: 1
+#| fig-width: 3
+#| fig-height: 4
+#| out-height: 125%
+require(magrittr)
+1:10 %>% plot()
+1:10 %>% plot(y = sin(1:10))
+sin(1:10) %>% plot(1:10, .)
+sin(1:10) |> plot(x = 1:10, y = _)
+
+```
+
+```{r}
+#| echo: false
+#| layout-nrow: 1
+#| fig-width: 3
+#| fig-height: 4
+#| out-height: 125%
+require(magrittr)
+1:10 %>% plot()
+1:10 %>% plot(y = sin(1:10))
+sin(1:10) %>% plot(1:10, .)
+sin(1:10) |> plot(x = 1:10, y = _)
+
+```
+
+
+
+
+
+
+## 代码编写规则
+
+```{r}
+#| eval: false
+
+# Strive for:
+short_flights <- flights |> filter(air_time < 60)
+# Avoid:
+SHORTFLIGHTS <- flights |> filter(air_time < 60)
+
+# Strive for
+z <- (a + b)^2 / d
+# Avoid
+z<-( a + b ) ^ 2/d
+
+# Strive for
+mean(x, na.rm = TRUE)
+# Avoid
+mean (x ,na.rm=TRUE)
+```
+
+## 练习
+
+```{r}
+#| eval: false
+flights|>filter(dest=="IAH")|>
+  group_by(year,month,day)|>summarize(n=n(),
+delay=mean(arr_delay,na.rm=TRUE))|>filter(n>10)
+
+flights|>filter(carrier=="UA",
+  dest%in%c("IAH","HOU"),sched_dep_time>
+0900,sched_arr_time<2000)|>group_by(flight)|>
+  summarize(delay=mean(
+arr_delay,na.rm=TRUE),cancelled=sum(is.na(arr_delay)),
+    n=n())|>filter(n>10)
+```
+
+
+## quarto
+
+![](../../image/quarto-flow.png) 
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+

SD/20240326_2_dataimport/_extensions

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+../../_extensions

SD/20240326_2_dataimport/index.qmd

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+---
+title: "Data import"
+subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
+author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
+date: today
+lang: zh
+format:
+  revealjs:
+    theme: dark
+    slide-number: true
+    chalkboard:
+      buttons: true
+    preview-links: auto
+    lang: zh
+    toc: true
+    toc-depth: 1
+    toc-title: 大纲
+    logo: ./_extensions/inst/img/ucaslogo.png
+    css: ./_extensions/inst/css/revealjs.css
+    pointer:
+      key: "p"
+      color: "#32cd32"
+      pointerSize: 18
+revealjs-plugins:
+  - pointer
+filters:
+  - d2
+---
+
+
+```{r}
+#| echo: false
+knitr::opts_chunk$set(echo = TRUE)
+source("../../coding/_common.R")
+library(tidyverse)
+```
+
+
+## tidyverse风格数据分析总体流程
+
+
+![](../../image/data-science/import.png) 
+
+
+## 导入csv数据
+
+```{r}
+read_lines("../../data/students.csv") |> cat(sep = "\n")
+```
+
+## 导入csv数据
+
+
+```{r}
+read_csv("../../data/students.csv") |>
+  knitr::kable()
+```
+
+
+## 读取数据
+
+```{r}
+(students <- read_csv("../../data/students.csv"))
+```
+
+
+## 读取数据
+
+```{r}
+#| message: false
+(students <- read_csv("../../data/students.csv", na = c("N/A", "")))
+```
+
+## 列名不要有空格
+
+```{r}
+students |> 
+  rename(
+    student_id = `Student ID`,
+    full_name = `Full Name`
+  )
+```
+
+## `janitor`处理空格
+
+```{r}
+#| message: false
+
+students |> janitor::clean_names()
+```
+
+## `janitor`处理空格
+
+```{r}
+students |>
+  janitor::clean_names() |>
+  mutate(meal_plan = factor(meal_plan))
+```
+
+## `janitor`处理空格
+
+```{r}
+students <- students |>
+  janitor::clean_names() |>
+  mutate(
+    meal_plan = factor(meal_plan),
+    age = parse_number(if_else(age == "five", "5", age))
+  )
+students
+```
+
+
+## 直接录入
+
+```{r}
+#| message: false
+
+read_csv(
+  "The first line of metadata
+  The second line of metadata
+  x,y,z
+  1,2,3",
+  skip = 2
+)
+```
+
+
+## 直接录入
+
+```{r}
+#| message: false
+read_csv(
+  "# A comment I want to skip
+  x,y,z
+  1,2,3",
+  comment = "#"
+)
+```
+
+
+## 指定列名
+
+```{r}
+#| message: false
+
+read_csv(
+  "1,2,3
+  4,5,6",
+  col_names = c("x", "y", "z")
+)
+```
+
+## 指定列的类型
+
+```{r}
+another_csv <- "
+x,y,z
+1,2,3"
+
+read_csv(
+  another_csv, 
+  col_types = cols(.default = col_character())
+)
+read_csv(
+  another_csv,
+  col_types = cols_only(x = col_character())
+)
+```
+
+
+## 练习
+
+```{r}
+#| eval: false
+
+read_csv("a,b\n1,2,3\n4,5,6")
+read_csv("a,b,c\n1,2\n1,2,3,4")
+read_csv("a,b\n\"1")
+read_csv("a,b\n1,2\na,b")
+read_csv("a;b\n1;3")
+```
+
+## 练习
+
+```{r}
+#| eval: false
+annoying <- tibble(
+  `1` = 1:10,
+  `2` = `1` * 2 + rnorm(length(`1`))
+)
+```
+
+
+
+## 批量读取
+
+```{r}
+#| message: false
+
+sales_files <- c("../../data/01-sales.csv",
+  "../../data/02-sales.csv",
+  "../../data/03-sales.csv")
+read_csv(sales_files, id = "file")
+```
+
+
+
+
+## 读取Excel，建议用`readxl`包
+
+```{r}
+(surveydf <- readxl::read_xlsx("../../data/survey.xlsx"))
+```
+
+## 读取Excel
+
+```{r}
+(airqualitydf <- readxl::read_xlsx("../../data/airquality.xlsx", sheet = 2))
+```
+
+
+
+## 批量读取
+
+```{r}
+sales_files <- list.files("../../data",
+  pattern = "sales\\.csv$", full.names = TRUE)
+sales_files
+```
+
+## 写入csv
+
+```{r}
+#| warning: false
+#| message: false
+students
+write_csv(students, "students-2.csv")
+read_csv("students-2.csv")
+```
+
+## 写入Excel
+
+```{r}
+writexl::write_xlsx(students, "../../data/writexldemo.xlsx")
+```
+
+## 读取数据库，以MySQL为例
+
+```{r}
+if (FALSE) {
+  conn <- cctdb::get_dbconn("nationalairquality")
+  DBI::dbListTables(conn)
+}
+```
+
+
+
+## 读取数据库，以MySQL为例
+
+```{r}
+if (FALSE) {
+  conn <- cctdb::get_dbconn("nationalairquality")
+  metadf <- tbl(conn, "metadf") |> 
+    head(100) |>
+    collect()
+  DBI::dbDisconnect(conn)
+  saveRDS(metadf, file = "../../data/metadfdemo.RDS")
+}
+metadf <- readRDS(file = "../../data/metadfdemo.RDS")
+lang <- "cn"
+metadf |>
+  ggplot(aes(lon, lat)) +
+geom_point(aes(fill = Area)) +
+dwfun::theme_sci()
+```
+
+## 练习
+
+```{r}
+#| include: false
+#| eval: false
+if (FALSE) {
+  conn <- cctdb::get_dbconn("nationalairquality")
+  metadf <- tbl(conn, "metadf") |> 
+    collect()
+  DBI::dbDisconnect(conn)
+  metanestdf <- metadf |>
+    nest(citydf = -Area)
+  names(metanestdf$citydf) <- metanestdf$Area
+  writexl::write_xlsx(metanestdf$citydf, path = "../../data/meta_city.xlsx")
+  dir.create("../../data/metacity/")
+  metanestdf |>
+    mutate(flag = purrr::map2(Area, citydf,
+      ~ writexl::write_xlsx(.y,
+        path = paste0("../../data/metacity/", .x, ".xlsx")
+      )))
+}
+```
+
+1. 从“../../data/sales.xlsx”读取第9到13行的数据
+2. 从“../../data/meta_city.xlsx”读取所有的数据，并保存至“../../data/meta_city_onetable1.xlsx”
+3. 从“../../data/metacity/”读取所有的数据，并保存至“../../data/meta_city_onetable2.xlsx”
+
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+

SD/20240326_2_dataimport/students-2.csv

@@ -0,0 +1,7 @@
+student_id,full_name,favourite_food,meal_plan,age
+1,Sunil Huffmann,Strawberry yoghurt,Lunch only,4
+2,Barclay Lynn,French fries,Lunch only,5
+3,Jayendra Lyne,NA,Breakfast and lunch,7
+4,Leon Rossini,Anchovies,Lunch only,NA
+5,Chidiegwu Dunkel,Pizza,Breakfast and lunch,5
+6,Güvenç Attila,Ice cream,Lunch only,6

SD/20240326_3_datatransform/_extensions

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+../../_extensions

SD/20240326_4_正则表达式/_extensions

@@ -0,0 +1 @@
+../../_extensions

SD/20240326_4_正则表达式/index.qmd

@@ -0,0 +1,153 @@
+---
+title: "正则表达式"
+subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
+author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
+date: today
+lang: zh
+format:
+  revealjs:
+    theme: dark
+    slide-number: true
+    chalkboard:
+      buttons: true
+    preview-links: auto
+    lang: zh
+    toc: true
+    toc-depth: 1
+    toc-title: 大纲
+    logo: ./_extensions/inst/img/ucaslogo.png
+    css: ./_extensions/inst/css/revealjs.css
+    pointer:
+      key: "p"
+      color: "#32cd32"
+      pointerSize: 18
+revealjs-plugins:
+  - pointer
+filters:
+  - d2
+---
+
+```{r}
+#| echo: false
+knitr::opts_chunk$set(echo = TRUE)
+source("../../coding/_common.R")
+library(nycflights13)
+library(tidyverse)
+
+```
+
+## 匹配数字
+
+### 匹配数字：
+
+- \d：匹配任意数字字符。
+- \d+：匹配一个或多个数字字符。
+- [0-9]: 匹配数字
+
+### 匹配字母：
+
+- \w：匹配任意字母、数字或下划线字符。
+- \w+：匹配一个或多个字母、数字或下划线字符。
+
+## 匹配数字
+
+### 匹配空白字符：
+
+- \s：匹配任意空白字符，包括空格、制表符、换行符等。
+- \s+：匹配一个或多个空白字符。
+
+### 匹配特定字符：
+
+- [abc]：匹配字符 a、b 或 c 中的任意一个。
+- [a-z]：匹配任意小写字母。
+- [A-Z]：匹配任意大写字母。
+- [0-9]：匹配任意数字。
+
+## 匹配数字
+
+### 匹配重复次数：
+
+- {n}：匹配前一个字符恰好 n 次。
+- {n,}：匹配前一个字符至少 n 次。
+- {n,m}：匹配前一个字符至少 n 次，但不超过 m 次。
+
+### 匹配边界：
+
+- ^：匹配字符串的开头。
+- $：匹配字符串的结尾。
+
+## 匹配数字
+
+### 匹配特殊字符：
+
+- \：转义特殊字符，使其按字面意义匹配。
+- .：匹配任意单个字符。
+- |：表示“或”关系，匹配两个或多个表达式之一。
+
+#### 匹配次数：
+
+- *：匹配前一个字符零次或多次。
+- +：匹配前一个字符一次或多次。
+- ?：匹配前一个字符零次或一次。
+
+## 匹配数字
+
+### 分组和捕获：
+
+- ()：将一系列模式组合成一个单元，可与特殊字符一起使用。
+
+### 预定义字符集：
+
+- \d：任意数字，相当于 [0-9]。
+- \w：任意字母、数字或下划线字符，相当于 [a-zA-Z0-9_]。
+- \s：任意空白字符，相当于 [ \t\n\r\f\v]。
+
+
+
+## 实例
+
+```{r}
+library(babynames)
+(x <- c("apple", "apppple", "abc123def"))
+x[str_detect(x, "[0-9]")]
+x[str_detect(x, "abc[0-9]+")]
+x[str_detect(x, "pp")]
+x[str_detect(x, "p{4}")]
+x[str_detect(x, "p{4}")]
+x[str_detect("apple", "ap*")]
+x[str_detect("apple", "app*")]
+x[str_detect("apple", "a..le")]
+```
+
+## 练习
+
+
+找出`babyname`中名字含有ar的行
+
+```{r}
+#| echo: false
+babynames |>
+  filter(str_detect(name, "ar"))
+```
+
+## 练习
+
+
+找出`babyname`中名字含有ar或者以ry结尾的行。
+
+```{r}
+#| echo: false
+babynames |>
+  filter(str_detect(name, "ar"))
+```
+
+![](../../image/data-science/transform.png) 
+
+
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+

SD/20240326_9_课后作业/_extensions

@@ -0,0 +1 @@
+../../_extensions

SD/20240326_9_课后作业/index.qmd

@@ -0,0 +1,50 @@
+---
+title: "课后作业7"
+subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
+author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
+date: today
+lang: zh
+format:
+  revealjs:
+    theme: dark
+    slide-number: true
+    chalkboard:
+      buttons: true
+    preview-links: auto
+    lang: zh
+    toc: true
+    toc-depth: 1
+    toc-title: 大纲
+    logo: ./_extensions/inst/img/ucaslogo.png
+    css: ./_extensions/inst/css/revealjs.css
+    pointer:
+      key: "p"
+      color: "#32cd32"
+      pointerSize: 18
+revealjs-plugins:
+  - pointer
+filters:
+  - d2
+---
+
+```{r}
+#| include: false
+#| cache: false
+lang <- "cn"
+require(tidyverse)
+require(learnr)
+```
+
+## 第7次课后作业
+
+1. 根据`airqualitydf.xlsx`，按采样点统计周末2天与工作日5天中空气质量指数（AQI）中位数，按城市统计低于所有采样点AQI30%分位值的采样点占比，列出上述占比最高的10个城市（不考虑采样点数低于5个的城市）。
+2. 按照不同城市分组，统计周末2天与工作日5天AQI中位数是否具有显著差异。
+
+作业模板：[第7次课后作业_模板.qmd](https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/main/SD/20240326_9_课后作业/第7次课后作业_模板.qmd)
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+

SD/20240326_9_课后作业/第7次课后作业_模板.qmd

@@ -0,0 +1,25 @@
+---
+title: 课后作业7
+author: 姓名
+format: html
+---
+
+
+# 示例问题，在R中输出`1+2+3+...+100`的结果
+
+采用`for`循环完成，代码如下：
+
+```{r}
+total <- 0
+for (i in 1:100) {
+  total <- total + i
+}
+total
+```
+
+
+# 根据`airqualitydf.xlsx`，按采样点统计周末2天与工作日5天中空气质量指数（AQI）中位数，按城市统计低于所有采样点AQI30%分位值的采样点占比，列出上述占比最高的10个城市（不考虑采样点数低于5个的城市）。
+
+
+
+# 按照不同城市分组，统计周末2天与工作日5天AQI中位数是否具有显著差异。

SD/makeslides.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# 2024-03-26
+
+# - part: whole-game.qmd
+#   chapters:
+#     - data-visualize.qmd
+#     - workflow-basics.qmd
+#     - data-transform.qmd
+#     - workflow-style.qmd
+#     - data-tidy.qmd
+#     - workflow-scripts.qmd
+#     - data-import.qmd
+#     - workflow-help.qmd
+
+# - part: visualize.qmd
+#   chapters:
+#     - layers.qmd
+#     - EDA.qmd
+#     - communication.qmd
+
+# 2024-03-28
+
+# - part: transform.qmd
+#   chapters:
+#     - logicals.qmd
+#     - numbers.qmd
+#     - strings.qmd
+#     - regexps.qmd
+#     - factors.qmd
+#     - datetimes.qmd
+#     - missing-values.qmd
+#     - joins.qmd
+#
+# - part: import.qmd
+#   chapters:
+#     - spreadsheets.qmd
+#     - databases.qmd
+#     - arrow.qmd
+#     - rectangling.qmd
+#     - webscraping.qmd
+
+# 2024-04-02
+
+# - part: program.qmd
+#   chapters:
+#     - functions.qmd
+#     - iteration.qmd
+#     - base-R.qmd
+#
+# - part: communicate.qmd
+#   chapters:
+#     - quarto.qmd
+#     - quarto-formats.qmd
+
+r4dsdir="$HOME/research/r4ds"
+
+datestr="20240326"
+
+mkdir 20240326_1_data-visualize
+mkdir 20240326_2_workflow-basics
+mkdir 20240326_3_data-transform
+mkdir 20240326_4_workflow-style
+mkdir 20240326_5_data-tidy
+mkdir 20240326_6_workflow-scripts
+mkdir 20240326_7_data-import
+mkdir 20240326_8_workflow-help
+
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/data-visualize.qmd >20240326_1_data-visualize/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/workflow-basics.qmd >20240326_2_workflow-basics/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/data-transform.qmd >20240326_3_data-transform/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/workflow-style.qmd >20240326_4_workflow-style/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/data-tidy.qmd >20240326_5_data-tidy/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/workflow-scripts.qmd >20240326_6_workflow-scripts/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/data-import.qmd >20240326_7_data-import/index.qmd
+awk '/```{r}/{print "\n##\n\n" $0; flag=1; next} /```/{flag=0} flag || /```/' "${r4dsdir}"/workflow-help.qmd >20240326_8_workflow-help/index.qmd
+
+find * -type d | grep 0326 | xargs -I{} cp -r ./20240321_0_R实践课程/_extensions {}/

_extensions/inst/css/revealjs.css

@@ -325,7 +325,7 @@ figure > figcaption {
 
 .reveal pre code:hover{
     font-size: xx-large;
-  line-height: 150%;
+  line-height: 120%;
 }
 
 section#title-slide p.subtitle {

_quarto.yml

@@ -1,52 +0,0 @@
-project:
-  type: website
-  output-dir: www/
-  render:
-    - "*.qmd"
-    - "!chp*.qmd"
-    - "!analysis/"
-    - "!*ignored.qmd"
-    - "!*ignored/"
-
-
-title: "区域水环境污染数据分析实践"
-lang: zh
-date: today
-bibliography: [BB/Ref.bib, BB/localRef.bib]
-
-website:
-  title: "Version: {{< var branch >}}"
-  reader-mode: true
-  site-url: https://drwater.rcees.ac.cn/{{< var projtype >}}/{{< var pubtype >}}/{{< var reponame >}}/@{{< var branch >}}
-  repo-url: https://drwater.rcees.ac.cn/git/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
-  repo-actions: [edit, source, issue]
-  page-navigation: true
-  page-footer: "Copyright 2024, [Ming Su](https://drwater.rcees.ac.cn)"
-  navbar:
-    background: "light"
-    search: true
-    right:
-      - icon: house
-        text: "Home"
-        file: index.qmd
-      - text: "Slides"
-        file: SD/index.qmd
-      - text: "About"
-        file: about.qmd
-      - icon: git
-        menu:
-          - text: Edit
-            url: https://drwater.rcees.ac.cn/git/{{< var projtype >}}/{{< var reponame >}}/_edit/
-          - text: Issue
-            url: https://drwater.rcees.ac.cn/git/{{< var projtype >}}/{{< var reponame >}}/issues
-  comments: 
-    hypothesis:
-      theme: clean
-      openSidebar: false
-
-format:
-  html:
-    theme: cosmo
-    css: _extensions/inst/css/style.css
-    toc: true
-    code-link: true

coding/_common.R

@@ -0,0 +1,55 @@
+set.seed(1014)
+
+# knitr::opts_chunk$set(
+# comment = "#>",
+# collapse = TRUE,
+# cache = TRUE,
+# fig.retina = 2,
+# fig.width = 6,
+# fig.asp = 2 / 3,
+# fig.show = "hold"
+# )
+
+# options(
+#   dplyr.print_min = 6,
+#   dplyr.print_max = 6,
+#   pillar.max_footer_lines = 2,
+#   pillar.min_chars = 15,
+#   stringr.view_n = 6,
+#   # Temporarily deactivate cli output for quarto
+#   cli.num_colors = 0,
+#   cli.hyperlink = FALSE,
+#   pillar.bold = TRUE,
+#   width = 77 # 80 - 3 for #> comment
+# )
+
+ggplot2::theme_set(ggplot2::theme_gray(12))
+
+# use results: "asis" when setting a status for a chapter
+status <- function(type) {
+  status <- switch(type,
+    polishing = "should be readable but is currently undergoing final polishing",
+    restructuring = "is undergoing heavy restructuring and may be confusing or incomplete",
+    drafting = "is currently a dumping ground for ideas, and we don't recommend reading it",
+    complete = "is largely complete and just needs final proof reading",
+    stop("Invalid `type`", call. = FALSE)
+  )
+
+  class <- switch(type,
+    polishing = "note",
+    restructuring = "important",
+    drafting = "important",
+    complete = "note"
+  )
+
+  cat(paste0(
+    "\n",
+    ":::: status\n",
+    "::: callout-", class, " \n",
+    "You are reading the work-in-progress second edition of R for Data Science. ",
+    "This chapter ", status, ". ",
+    "You can find the complete first edition at <https://r4ds.had.co.nz>.\n",
+    ":::\n",
+    "::::\n"
+  ))
+}

data/01-sales.csv

@@ -0,0 +1,8 @@
+month,year,brand,item,n
+January,2019,1,1234,3
+January,2019,1,8721,9
+January,2019,1,1822,2
+January,2019,2,3333,1
+January,2019,2,2156,9
+January,2019,2,3987,6
+January,2019,2,3827,6

data/02-sales.csv

@@ -0,0 +1,7 @@
+month,year,brand,item,n
+February,2019,1,1234,8
+February,2019,1,8721,2
+February,2019,1,1822,3
+February,2019,2,3333,1
+February,2019,2,2156,3
+February,2019,2,3987,6

data/03-sales.csv

@@ -0,0 +1,7 @@
+month,year,brand,item,n
+March,2019,1,1234,3
+March,2019,1,3627,1
+March,2019,1,8820,3
+March,2019,2,7253,1
+March,2019,2,8766,3
+March,2019,2,8288,6

data/gapminder.R

@@ -0,0 +1,20 @@
+
+
+repurrrsive::gap_simple |>
+  count(year)
+
+by_year <- repurrrsive::gap_simple |>
+  group_by(year)
+paths <- by_year |>
+  group_keys() |>
+  mutate(path = str_glue("data/gapminder/{year}.xlsx")) |>
+  pull()
+paths
+
+years <- by_year |>
+  group_split() |>
+  map(\(df) select(df, -year))
+
+dir.create("data/gapminder")
+
+walk2(years, paths, writexl::write_xlsx)