add some lesson for lesson6

SD/1.1_R语言介绍/_demo.qmd

@@ -0,0 +1,91 @@
+---
+title: "Lesson 6"
+format: html
+---
+
+
+
+
+```{r}
+
+https://rs1.drwater.net
+
+username: 
+  - ruser01
+  - ruser02
+  - ruser03
+  - ruser04
+  - ruser05
+  - ruser06
+
+RWEP2025
+
+```
+
+
+# 安装包
+
+
+```{r}
+install.packages("tidyverse")
+
+x <- c(1:10, NA)
+
+hist(x)
+
+mean(x, na.rm = TRUE)
+
+median(x, na.rm = TRUE)
+
+sd(x, na.rm = TRUE)
+
+
+for(i in 1:10){
+  print(i)
+}
+
+
+x + y + x * y
+
+myfunc <- function(x, y = 3) {
+  x + y + x * y
+}
+
+
+myfunc(1, 2)
+
+
+myfunc(10)
+
+
+c(FALSE, 2, 1:3, 3) 
+
+c(FALSE, 2, 1:3, 3) > 1
+
+all(c(FALSE, 2, 1:3, 3) > 1)
+
+
+c(1L,2L,3L)
+
+any(c(FALSE, 2, 1:3, 3) > 1)
+
+
+x <- 10
+
+sin(x) = ?
+
+paste("sin(x) = ", sin(x), sep = " ")
+
+paste0("sin(x) = ", sin(x))
+
+
+substr("Monday", 1, 3)
+
+
+
+```
+
+
+
+
+

SD/1.2_R语言语法基础/index.qmd

@@ -264,6 +264,9 @@ t.test(x, y)
 wilcox.test(x, y)
 ```
 
+
+### [什么是 Wilcoxon-Mann-Whitney检验？](https://zhuanlan.zhihu.com/p/613524533）
+
 ## 统计函数
 
 ### 创建向量的直方图

SD/2.1_codestyle/_extensions

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

SD/2.1_codestyle/index.qmd

@@ -0,0 +1,162 @@
+---
+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)
+
+```
+
+## 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)
+
+```
+
+## quarto
+
+![](../../image/quarto-flow.png) 
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+

SD/2.2_dataimport/_extensions

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

SD/2.2_dataimport/index.qmd

@@ -0,0 +1,324 @@
+---
+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}
+#| eval: false
+metadf <- readxl::read_xlsx("../../data/airquality.xlsx")
+dir.create("../../data/metacity2/")
+metadf |>
+  nest(sitedf = -site) |>
+  mutate(flag = purrr::map2(site, sitedf,
+    ~ writexl::write_xlsx(.y, paste0("../../data/metacity2/", .x, ".xlsx"))))
+```
+
+
+## 练习
+
+```{r}
+#| include: false
+#| eval: false
+if (FALSE) {
+  require(tidyverse)
+  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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`

SD/2.2_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

_quarto.yml

@@ -9,6 +9,7 @@ project:
     - "!*ignored/"
     - "!coding/"
     - "!SD/_*/"
+    - "!SD/*/_*.qmd"
 
 title: "区域水环境污染数据分析实践"
 lang: zh