render compile

.gitignore

@@ -7,3 +7,4 @@ _variables.yml
 _freeze/
 *_cache/
 *_files/
+SD/_*/

.source_state

@@ -0,0 +1 @@
+454c267b732cda3ca58332ab3883bec6

Makefile

@@ -0,0 +1,382 @@
+# Makefile for Quarto Project Automation
+# Detect OS
+HOSTNAME := $(shell hostname)
+OS := $(shell uname | tr A-Z a-z)
+ifeq ($(OS), darwin)
+    SEDI := sed -i ''
+    OS := OSX
+else ifeq ($(OS), linux)
+    SEDI := sed -i
+    OS := linux
+else
+    $(error Unknown operating system)
+endif
+
+# Fetch Git branch and project details
+branchname := $(shell git branch --show-current)
+reponame := $(shell basename $(shell git rev-parse --show-toplevel))
+projtype := $(shell basename $(shell dirname $(shell git rev-parse --show-toplevel)))
+pubtype := $(if $(findstring PUB,$(branchname)),public,protected)
+remotedir := dwuser@drwater.net:/home/www/drc/$(projtype)/$(pubtype)/$(reponame)/$(branchname)
+outputdir := $(shell awk -F': *' '/^ *output-dir:/ {print $$2 "/" }' ./_quarto.yml)
+siteurl := https://drc.drwater.net/$(projtype)/$(pubtype)/$(reponame)/$(branchname)
+
+branchnames := "TX\|FJ\|YF\|ZY\|WW\|JB\|YY\|YJ\|DYF"
+
+# Variables for colors and port
+bcolor := grey
+port := 4199
+
+# Set background color based on branch name
+ifeq ($(findstring R1,$(branchname)),R1)
+    bcolor := orange
+else ifeq ($(findstring R2,$(branchname)),R2)
+    bcolor := lightblue
+else ifeq ($(findstring R3,$(branchname)),R3)
+    bcolor := lightgreen
+else ifeq ($(findstring PUB,$(branchname)),PUB)
+    bcolor := light
+endif
+
+# Set port based on branch name
+branch_ports := main:4200 SM:4201 TX:4202 FJ:4203 YF:4204 ZY:4205 WW:4206 JB:4207 YY:4208 YJ:4209 DYF:4210
+port := $(shell echo $(branch_ports) | tr " " "\n" | grep -E "^$(branchname):" | sed -E 's/^$(branchname):([0-9]+)/\1/')
+port := $(if $(port),$(port),4199)
+
+# Define the state file
+STATE_FILE := .source_state
+
+# checkfile
+GREPSTR := " \|(\|)\|^submit\|^analysis\|_cache\|_freeze\|^site_libs\|^www"
+
+# Default target
+.PHONY: all preview readme rsync local clean upload fix_links force check_git_status
+
+all: local upload clean commit push
+	
+force: updrefbib check_git_status updvariable render
+
+local: updrefbib check_git_status updvariable lazyrender
+
+updmakefile:
+	@if [ "$(OS)" = "OSX" ] && [ "$(HOSTNAME)" = "max" ]; then \
+		echo "基于 $$HOME/bin/publish2dw.Makefile 更新本项目 Makefile..."; \
+		cp "$$HOME/bin/publish2dw.Makefile" "./Makefile"; \
+		git add "Makefile" && git commit -m "Update Makefile"; \
+		echo "本项目Makefile更新完成."; \
+	else \
+		echo "Makefile 无需在本系统上更新."; \
+	fi
+
+
+updrefbib:
+	@if [ "$(OS)" = "OSX" ] && [ "$(HOSTNAME)" = "max" ]; then \
+		echo "更新本项目参考文献..."; \
+		cp "$$HOME/literature/Ref.bib" "./BB/"; \
+		echo "推送本地参考文献到远程服务器..."; \
+		rsync -azvu --progress "$$HOME/literature/Ref.bib" "drwater.net:/home/www/drc/datapool/public/BB/Ref.bib"; \
+		echo "本项目参考文献更新完成."; \
+	else \
+	  echo "检查网络连通性..."; \
+		if ping -c 1 -W 1 drc.drwater.net > /dev/null 2>&1; then \
+			echo "网络正常，更新本项目参考文献..."; \
+			wget -O BB/Ref.bib "https://drc.drwater.net/datapool/public/BB/Ref.bib"; \
+			echo "本项目参考文献更新完成."; \
+		else \
+			echo "网络不可用，跳过参考文献更新."; \
+		fi; \
+	fi; \
+	git add BB/Ref.bib; \
+	if [ "$$(git diff --cached)" ]; then \
+		git commit -m "Update Ref.bib"; \
+	fi
+
+check_git_status:
+	@uncommitted=$$(git status --porcelain); \
+	if [ -n "$$uncommitted" ]; then \
+	  git status; \
+		read -p "当前存在未提交的修改（如上），是否要提交？(Y/N, default is N): " answer; \
+		answer=$${answer:-N}; \
+		if [ "$$answer" = "Y" ] || [ "$$answer" = "y" ]; then \
+			read -p "请输入修改说明: " message; \
+			git add . && git commit -m "$$message"; \
+		else \
+			echo "未提交，如后续操作为pull，则无法继续"; \
+		fi; \
+	fi
+
+
+
+# Lazy render with hash checking
+lazyrender:
+	@current_hash=$$(find $(shell git ls-files "*.qmd" "_*.yml" "*.pdf" "*.svg" "*.png" | grep -v $(GREPSTR)) -exec cat {} + | md5sum | awk '{print $$1}'); \
+	if [ ! -f $(STATE_FILE) ] || [ "$$current_hash" != "$$(cat $(STATE_FILE))" ]; then \
+		echo "源文件发生变化, 重新编译..."; \
+		echo "$$current_hash" > $(STATE_FILE); \
+		$(MAKE) render; \
+	else \
+		echo "源文件无变化, 跳过编译..."; \
+		exit 0; \
+	fi
+
+# Render target
+render:
+	@quarto render
+
+commit:
+	@echo "提交修改(commit)..."; \
+		git add .; \
+		if [ -n "$$(git diff --cached)" ]; then \
+		git commit -m "render compile"; \
+		else \
+		echo "没有修改记录，跳过."; \
+		fi; \
+
+# Pull changes from the specified branch based on the current branch
+pull:
+	@echo "从远程拉取项目更新..."; \
+		$(MAKE) check_git_status; \
+		git pull; \
+		current_branch=$$(git rev-parse --abbrev-ref HEAD); \
+		if [ "$$current_branch" = main ]; then \
+		  echo "当前分枝为$$current_branch."; \
+			remote_branch=$$(git branch --remote | grep -v 'main' | grep $(branchnames) | awk '{print $$1}' | sed 's/origin\///' | head -n 1); \
+			if [ -n "$$remote_branch" ]; then \
+		    echo "尝试从远程分枝$$remote_branch 拉取更新..."; \
+				git pull --rebase origin $$remote_branch; \
+			else \
+				echo "远程无可用分支$$remote_branch."; \
+			fi; \
+			else \
+			echo "尝试将远程main分枝合并至本地$$current_branch 分枝."; \
+			git pull --rebase origin main; \
+		fi
+
+# Pull changes from the main branch
+pullmain:
+	$(MAKE) check_git_status; \
+		@current_branch=$$(git rev-parse --abbrev-ref HEAD); \
+		@echo "尝试将远程main分枝合并至本地$$current_branch 分枝."; \
+		git pull --rebase origin main; \
+
+push:
+	@echo "推送到远程..."; \
+		git push
+
+filehash:
+	@current_hash=$$(find $(shell git ls-files "*.qmd" "_*.yml" "*.pdf" "*.svg" "*.png" | grep -v $(GREPSTR)) -exec cat {} + | md5sum | awk '{print $$1}'); \
+	echo "$$current_hash" > $(STATE_FILE)
+
+# Preview the site on a specific port
+preview:
+	@quarto preview --port $(port)
+
+# Generate README.md
+readme:
+	@quarto render index.qmd -t markdown -o README.md
+	@sed -e '/^---/,/^---/d' "$(outputdir)/README.md" > README.md
+	@rm "$(outputdir)/README.md"
+
+# Sync files with remote server
+rsync:
+	@rsync -azvu --progress --delete -r "$(outputdir)" "$(remotedir)"
+
+# Open local site
+open:
+	@if [ "$(OS)" = "OSX" ]; then open "$(outputdir)/index.html"; fi
+
+# Clean unnecessary files
+clean:
+	@rm -f ./*.spl  ./*.bbl ./*.blg ./*.log ./*.tex ./*.bcf ./*.tex.sedbak ./*.fdb_latexmk
+
+# Upload files to server and fix links
+upload: backupdocx
+	@mkdir -p "$(outputdir)" && chmod -R 2775 "$(outputdir)"
+	@$(MAKE) fix_links
+	@if rsync -azvu --progress --delete -r "$(outputdir)" "$(remotedir)"; then \
+		if [ "$(OS)" = "OSX" ]; then \
+			open "$(siteurl)" 2>/dev/null; \
+		fi; \
+	else \
+		echo "Rsync failed. Attempting alternative upload method..."; \
+		mkdir -p "$(reponame)"; \
+		rsync -azvu --progress --delete -r "$(reponame)" "$(dir $(remotedir))"; \
+		rm -rf "$(reponame)"; \
+		rsync -azvu --progress --delete -r "$(outputdir)" "$(remotedir)"; \
+		if [ "$(OS)" = "OSX" ]; then \
+			open "$(siteurl)" 2>/dev/null; \
+		fi; \
+	fi
+
+backupdocx:
+	@echo "备份MS.docx文件..."; \
+	currentcommithash=$$(git rev-parse --short HEAD); \
+	datetime=$$(git show -s --format=%ci $$currentcommithash | sed 's/[-: ]//g' | cut -c3-12); \
+	mkdir -p TC/MS/; \
+	existing_file=$$(find TC/MS -name "MS*.docx" -exec cmp -s www/MS/MS.docx {} \; -print -quit); \
+	if [ -n "$$existing_file" ]; then \
+		echo "与www/MS/MS.docx 内容相同的备份文件已存在: $$existing_file"; \
+		echo "无需备份."; \
+	else \
+		if [ ! -e TC/MS/MS$${datetime}_$${currentcommithash}.docx ]; then \
+			cp www/MS/MS.docx TC/MS/MS$${datetime}_$${currentcommithash}.docx; \
+			echo "备份TC/MS/MS$${datetime}_$${currentcommithash}.docx完成."; \
+			git add TC/MS/MS$${datetime}_$${currentcommithash}.docx; \
+			if [ "$$(git diff --cached)" ]; then \
+				git commit -m "备份TC/MS/MS$${datetime}_$${currentcommithash}.docx"; \
+			fi; \
+		else \
+			echo "TC/MS/MS$${datetime}_$${currentcommithash}.docx已存在，无需备份."; \
+		fi; \
+	fi;
+
+
+trackchange:
+	@if [ "$(projtype)" != "manuscript" ]; then \
+	exit 0; \
+	fi; \
+	echo "选择两个提交以比较文档..."; \
+	hashes=$$(git log --pretty=format:'%h: %s BY %an (%ar)' \
+	| grep -E "$$(ls TC/MS/*.docx | xargs -n1 basename | sed -E 's/MS.*_([0-9a-f]+)\.docx/\1/' | tr '\n' '|')SMT_】" \
+	| fzf --multi --reverse --preview="echo {}" ); \
+	echo $$hashes; \
+	hash1=$$(echo $$hashes | sed -e 's/) \([a-z0-9]\{7\}:\)/)\n\1/g' | tail -n 1 | awk '{print $$1}' | tr -d ':'); \
+	hash1=$$(git rev-parse --short $${hash1}^); \
+	datetime1=$$(git show -s --format=%ci $$hash1 | sed 's/[-: ]//g' | cut -c3-12); \
+	hash2=$$(echo $$hashes | sed -e 's/) \([a-z0-9]\{7\}:\)/)\n\1/g' | head -n 1 | awk '{print $$1}' | tr -d ':'); \
+	hash2=$$(git rev-parse --short $${hash2}^); \
+	datetime2=$$(git show -s --format=%ci $$hash2 | sed 's/[-: ]//g' | cut -c3-12); \
+	if [ -z "$$hash1" ] || [ -z "$$hash2" ]; then \
+	echo "必须选择两个提交."; \
+	exit 1; \
+	fi; \
+	doc1="TC/MS/MS$${datetime1}_$$hash1.docx"; \
+	echo "$$doc1"; \
+	doc2="TC/MS/MS$${datetime2}_$$hash2.docx"; \
+	echo "$$doc2"; \
+	if [ -f "$$doc1" ] && [ -f "$$doc2" ] && [ "$$doc1" != "$$doc2" ]; then \
+	echo "打开文件: $$doc1 和 $$doc2"; \
+	open "$$doc1" "$$doc2"; \
+	printf "MS$${datetime1}-$${datetime2}_$${hash1}-$${hash2}" | pbcopy; \
+	echo "请在word中对比两个版本形成带修改痕迹的版本，并保存至TC/MS$${datetime1}-$${datetime2}_$${hash1}-$${hash2}.docx!"; \
+	else \
+	echo "一个或两个文件不存在: $$doc1, $$doc2"; \
+	exit 1; \
+	fi
+
+# Fix links in www directory
+fix_links:
+	@find ./www -type f -name "*.html" -exec sed -i.bak \
+		-e "s/{{< var branch >}}/$(branchname)/g" \
+		-e "s/{{< var pubtype >}}/$(pubtype)/g" \
+		-e "s/{{< var projtype >}}/$(projtype)/g" \
+		-e "s/{{< var reponame >}}/$(reponame)/g" \
+		-e "s/$(reponame)\/blob/$(reponame)\/raw\/branch/g" \
+		-e "s/$(reponame)\/edit/$(reponame)\/_edit/g" {} +
+	@find ./www -type f -name "*.bak" -exec rm {} +
+
+updvariable:
+	@touch _variables.yml  # 如果文件不存在则创建
+	@grep -q '^reponame:' _variables.yml || echo "reponame: $(reponame)" >> _variables.yml
+	@if grep -q '^reponame:' _variables.yml; then \
+		$(SEDI) 's/^reponame:.*/reponame: $(reponame)/' _variables.yml; \
+	else \
+		echo "reponame: $(reponame)" >> _variables.yml; \
+	fi
+	@grep -q '^projtype:' _variables.yml || echo "projtype: $(projtype)" >> _variables.yml
+	@if grep -q '^projtype:' _variables.yml; then \
+		$(SEDI) 's/^projtype:.*/projtype: $(projtype)/' _variables.yml; \
+	else \
+		echo "projtype: $(projtype)" >> _variables.yml; \
+	fi
+	@grep -q '^branch:' _variables.yml || echo "branch: $(branchname)" >> _variables.yml
+	@if grep -q '^branch:' _variables.yml; then \
+		$(SEDI) 's/^branch:.*/branch: $(branchname)/' _variables.yml; \
+	else \
+		echo "branch: $(branchname)" >> _variables.yml; \
+	fi
+	@grep -q '^pubtype:' _variables.yml || echo "pubtype: $(pubtype)" >> _variables.yml
+	@if grep -q '^pubtype:' _variables.yml; then \
+		$(SEDI) 's/^pubtype:.*/pubtype: $(pubtype)/' _variables.yml; \
+	else \
+		echo "pubtype: $(pubtype)" >> _variables.yml; \
+	fi
+	@grep -q '^nwAB:' _variables.yml || echo "nwAB: $(nwAB)" >> _variables.yml
+	@if grep -q '^nwAB:' _variables.yml; then \
+		$(SEDI) 's/^nwAB:.*/nwAB: $(nwAB)/' _variables.yml; \
+	else \
+		echo "nwAB: $(nwAB)" >> _variables.yml; \
+	fi
+	@grep -q '^nwMS:' _variables.yml || echo "nwMS: $(nwMS)" >> _variables.yml
+	@if grep -q '^nwMS:' _variables.yml; then \
+		$(SEDI) 's/^nwMS:.*/nwMS: $(nwMS)/' _variables.yml; \
+	else \
+		echo "nwMS: $(nwMS)" >> _variables.yml; \
+	fi
+	@grep -q '^figtblMS:' _variables.yml || echo "figtblMS: $(figtblMS)" >> _variables.yml
+	@if grep -q '^figtblMS:' _variables.yml; then \
+		$(SEDI) 's/^figtblMS:.*/figtblMS: $(figtblMS)/' _variables.yml; \
+	else \
+		echo "figtblMS: $(figtblMS)" >> _variables.yml; \
+	fi
+	@grep -q '^figtblSM:' _variables.yml || echo "figtblSM: $(figtblSM)" >> _variables.yml
+	@if grep -q '^figtblSM:' _variables.yml; then \
+		$(SEDI) 's/^figtblSM:.*/figtblSM: $(figtblSM)/' _variables.yml; \
+	else \
+		echo "figtblSM: $(figtblSM)" >> _variables.yml; \
+	fi
+	@mkpapervar
+
+
+# Help: list all available commands with descriptions (English and Chinese)
+help:
+	@echo "Makefile for Quarto Project Automation"
+	@echo "======================================="
+	@echo "Available targets (English):"
+	@echo ""
+	@echo "  make all           - Execute local build, upload, clean, and commit"
+	@echo "  make force         - Force render, hash update, upload, clean, and commit"
+	@echo "  make local         - Check git status and perform a lazy render if changes detected"
+	@echo "  make check_git_status - Check for uncommitted changes and ask to commit them"
+	@echo "  make lazyrender    - Render if source files have changed based on hash comparison"
+	@echo "  make render        - Force Quarto to render the project"
+	@echo "  make commit        - Commit changes if no previous uncommitted changes"
+	@echo "  make filehash      - Generate and store the file hash of source files"
+	@echo "  make preview       - Preview the site locally on the specific port (default: 4199)"
+	@echo "  make readme        - Render README.md from Quarto index.qmd"
+	@echo "  make rsync         - Sync output files with the remote server"
+	@echo "  make open          - Open the generated site locally in the browser"
+	@echo "  make clean         - Clean up unnecessary files"
+	@echo "  make upload        - Upload files to the server and fix links"
+	@echo "  make fix_links     - Fix HTML links in the 'www' directory for the remote server"
+	@echo "  make updmakefile   - Update the Makefile"
+	@echo "  make help          - Display this help message"
+	@echo ""
+	@echo "Available targets (中文):"
+	@echo ""
+	@echo "  make all           - 执行本地构建、上传、清理和提交"
+	@echo "  make force         - 强制渲染、更新哈希、上传、清理并提交"
+	@echo "  make local         - 检查Git状态，若检测到更改则进行懒惰渲染"
+	@echo "  make check_git_status - 检查未提交的更改，并询问是否提交"
+	@echo "  make lazyrender    - 如果源文件发生更改，则根据哈希比较进行渲染"
+	@echo "  make render        - 强制 Quarto 渲染项目"
+	@echo "  make commit        - 如果没有未提交的更改则提交"
+	@echo "  make filehash      - 生成并存储源文件的哈希值"
+	@echo "  make preview       - 本地在特定端口预览网站 (默认: 4199)"
+	@echo "  make readme        - 从 Quarto 的 index.qmd 生成 README.md"
+	@echo "  make rsync         - 将输出文件同步到远程服务器"
+	@echo "  make open          - 在浏览器中打开生成的网站"
+	@echo "  make clean         - 清理不必要的文件"
+	@echo "  make upload        - 上传文件到服务器并修复链接"
+	@echo "  make fix_links     - 修复 'www' 目录中的 HTML 链接"
+	@echo "  make updmakefile   - 更新本项目 Makefile"
+	@echo "  make help          - 显示此帮助信息"
+	@echo ""
+	@echo "Environment variables (English and 中文):"
+	@echo "  bcolor             - Background color based on branch name (基于分支名的背景颜色)"
+	@echo "  port               - Port number based on branch name (基于分支名的端口号)"
+	@echo "  STATE_FILE         - File for storing hash state of source files (用于存储源文件哈希状态的文件)"
+	@echo "  siteurl            - The URL where the site will be hosted (网站托管的 URL)"
+	@echo ""
+
+

SD/0_R实践课程/index.qmd

@@ -47,9 +47,8 @@ knitr::opts_chunk$set(echo = TRUE)
 ### 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)
+- 网页公开：[https://drc.drwater.net/course/public/RWEP/PUB/index.html](https://drc.drwater.net/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)
+- 课件代码：[https://git.drwater.net/course/RWEP.git](https://git.drwater.net/course/RWEP.git)
-- 代码web界面：[https://on.tty-share.com/s/ny3JVrMuvUNOmnuioS3I7YEeVCi5Hk3Qc9vgz2QdX0FE2cYAQZFW2MUOkQyG0P5ZUR8/](https://on.tty-share.com/s/ny3JVrMuvUNOmnuioS3I7YEeVCi5Hk3Qc9vgz2QdX0FE2cYAQZFW2MUOkQyG0P5ZUR8/)
 
 ## 如何学习接下来的内容？
 
@@ -67,7 +66,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 ## Rstudio Server使用
 
-- 服务网址：[https://drwater.rcees.ac.cn/rs1/](https://drwater.rcees.ac.cn/rs1/)
+- 服务网址：[https://rs1.drwater.net/](https://rs1.drwater.net/)
 - 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

SD/1.1_R语言介绍/_demo.qmd

@@ -0,0 +1,138 @@
+---
+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)
+
+
+
+```
+
+
+# tidy
+
+
+```{r}
+require(readxl)
+
+aqdf <-readxl::read_xlsx("../../data/airquality.xlsx", sheet = "metadf")
+
+# install.packages("skimr")
+
+aqdf |>
+  skimr::skim()
+
+# base
+
+# tidyverse
+
+aqdf |>
+  dplyr::group_by(Area) |>
+  dplyr::summarize(
+    n = n(),
+    lon.mean = mean(lon, na.rm = TRUE),
+    lon.sd = sd(lat, na.rm = TRUE)
+  ) |>
+  dplyr::filter(Area %in% c("北京市", "天津市", "上海市", "重庆市")) |>
+  ggplot(aes(x = n, y = lon.mean)) +
+  geom_point() +
+  geom_line() +
+  geom_errorbar(
+    aes(ymin = lon.mean - lon.sd,
+      ymax = lon.mean + lon.sd)
+  )
+
+
+
+
+
+
+
+readxl::read_xlsx("./airquality.xlsx")
+
+flights|>
+  filter(dest=="IAH")|>
+  group_by(year,month,day)|>summarize(n=n(),
+delay=mean(arr_delay,na.rm=TRUE))|>filter(n>10)
+
+```
+
+
+

SD/1.1_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 = "../")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`

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
@@ -792,4 +795,4 @@ names(Y) <- c("colA", "colB", "colC")
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`

SD/1.3_Excel基础/index.qmd

@@ -37,7 +37,7 @@ require(learnr)
 
 ## 下载excel文件
 
-[https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/main/data/airquality.xlsx](https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/main/data/airquality.xlsx)
+[https://git.drwater.net/course/RWEP/raw/branch/main/data/airquality.xlsx](https://git.drwater.net/course/RWEP/raw/branch/main/data/airquality.xlsx)
 
 
 ## Tidy data

SD/1.9_课后作业6/data.csv

@@ -0,0 +1,21 @@
+name,age,score
+Alice,25,85
+Bob,30,92
+Charlie,28,89
+David,22,95
+Eva,35,87
+Frank,27,91
+Grace,29,88
+Helen,26,93
+Ivan,31,86
+Jack,24,94
+Kelly,32,89
+Lily,28,90
+Mike,33,85
+Nancy,27,92
+Olivia,34,88
+Peter,29,93
+Queen,25,89
+Ryan,30,94
+Samantha,26,91
+Tom,31,87

SD/1.9_课后作业6/index.qmd

@@ -79,5 +79,5 @@ Tom,31,87
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
 

SD/2.2_dataimport/index.qmd

@@ -321,5 +321,4 @@ if (FALSE) {
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
-

SD/2.3_datatransform/index.qmd

@@ -323,5 +323,5 @@ flights |>
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
 

SD/20240402_9_课后作业/index.qmd

@@ -1,49 +0,0 @@
----
-title: "课后作业9"
-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9次课后作业
-
-自选数据集，使用R语言开展不同因子（如年份、季节、处理方式等）间某指标的差异分析，采用图表方式形成简要报告。
-
-作业模板：[第9次课后作业_模板.qmd](https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/main/SD/20240402_9_课后作业/第9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/20240402_9_课后作业/第9次课后作业_模板.qmd

@@ -1,8 +0,0 @@
----
-title: 课后作业9
-author: 姓名
-format: html
----
-
-要求：自选数据集，使用R语言开展不同因子间（如年份、季节、处理方式等）某指标的差异分析，采用图表+文字说明等方式形成简要报告。
-

SD/20240409_2_大数据分析工具/_extensions

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

SD/3.1_datatransform/index.qmd

@@ -945,5 +945,5 @@ semi_join(df1, df2, by = "id")
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
 

SD/3.9_课后作业8/index.qmd

@@ -43,7 +43,7 @@ require(learnr)
 1. 根据`airqualitydf.xlsx`，按采样点统计白天（8:00-20:00）与夜晚（20:00-8:00）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，统计白天与夜晚AQI中位数是否具有显著差异。
 
-作业模板：[第8次课后作业_模板.qmd](https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/main/SD/20240328_9_课后作业/第8次课后作业_模板.qmd)
+作业模板：[第8次课后作业_模板.qmd](https://git.drwater.net/course/RWEP/raw/branch/main/SD/20240328_9_课后作业/第8次课后作业_模板.qmd)
 
 ## 示例代码
 
@@ -62,5 +62,5 @@ 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
 

SD/3.9_课后作业8/第8次课后作业_模板.qmd

@@ -14,7 +14,7 @@ format: html
 # 下载至临时文件
 if (FALSE) {
   tmpxlsxpath <- file.path(tempdir(), "airquality.xlsx")
-  download.file("https://drwater.rcees.ac.cn/git/course/RWEP/raw/branch/PUB/data/airquality.xlsx",
+  download.file("https://git.drwater.net/course/RWEP/raw/branch/PUB/data/airquality.xlsx",
     destfile = tmpxlsxpath)
   airqualitydf <- readxl::read_xlsx(tmpxlsxpath, sheet = 2)
   metadf <- readxl::read_xlsx(tmpxlsxpath, sheet = 1)
@@ -118,6 +118,8 @@ if (FALSE) {
   saveRDS(testdf, "./testdf.RDS")
 }
 
+if (FALSE) {
+
 lang <- "cn"
 require(dwfun)
 require(rmdify)
@@ -144,5 +146,7 @@ testdf |>
   pull(gp)
 
 
+}
+
 ```
 

SD/4.1_datavisualize/index.qmd

@@ -3934,5 +3934,5 @@ p
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
 

SD/4.2_实践部分/index.qmd

@@ -100,5 +100,4 @@ geom_bar(position = "fill")
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
-

SD/5.1_model/index.qmd

@@ -47,7 +47,8 @@ hexes <- function(..., size = 64) {
   right <- (seq_along(x) - 1) * size
   res <- glue::glue(
     '![](hexes/<x>.png){.absolute top=-20 right=<right> width="<size>" height="<size * 1.16>"}',
-    .open = "<", .close = ">"
+    .open = "<",
+    .close = ">"
   )
   paste0(res, collapse = " ")
 }
@@ -65,11 +66,10 @@ theme_set(theme_bw())
 options(cli.width = 70, ggplot2.discrete.fill = c("#7e96d5", "#de6c4e"))
 
 train_color <- "#1a162d"
-test_color  <- "#cd4173"
+test_color <- "#cd4173"
-data_color  <- "#767381"
+data_color <- "#767381"
 assess_color <- "#84cae1"
 splits_pal <- c(data_color, train_color, test_color)
-
 ```
 
 
@@ -152,10 +152,27 @@ knitr::include_graphics("images/whole-game-final-performance.jpg")
 
 # Install the packages for the workshop
 pkgs <-
-  c("bonsai", "doParallel", "embed", "finetune", "lightgbm", "lme4",
+  c(
-    "plumber", "probably", "ranger", "rpart", "rpart.plot", "rules",
+    "bonsai",
-    "splines2", "stacks", "text2vec", "textrecipes", "tidymodels", 
+    "doParallel",
-    "vetiver", "remotes")
+    "embed",
+    "finetune",
+    "lightgbm",
+    "lme4",
+    "plumber",
+    "probably",
+    "ranger",
+    "rpart",
+    "rpart.plot",
+    "rules",
+    "splines2",
+    "stacks",
+    "text2vec",
+    "textrecipes",
+    "tidymodels",
+    "vetiver",
+    "remotes"
+  )
 
 install.packages(pkgs)
 ```
@@ -197,26 +214,34 @@ taxi
 #|
 set.seed(123)
 library(forcats)
-one_split <- slice(taxi, 1:30) %>% 
+require(tidymodels)
-  initial_split() %>% 
+require(tidyverse)
-  tidy() %>% 
+one_split <- taxi |>
-  add_row(Row = 1:30, Data = "Original") %>% 
+  dplyr::slice(1:30) |>
-  mutate(Data = case_when(
+  rsample::initial_split() |>
-    Data == "Analysis" ~ "Training",
+  generics::tidy() |>
-    Data == "Assessment" ~ "Testing",
+  tibble::add_row(Row = 1:30, Data = "Original") |>
-    TRUE ~ Data
+  dplyr::mutate(
-  )) %>% 
+    Data = case_when(
-  mutate(Data = factor(Data, levels = c("Original", "Training", "Testing")))
+      Data == "Analysis" ~ "Training",
+      Data == "Assessment" ~ "Testing",
+      TRUE ~ Data
+    )
+  ) |>
+  dplyr::mutate(
+    Data = factor(Data, levels = c("Original", "Training", "Testing"))
+  )
 all_split <-
   ggplot(one_split, aes(x = Row, y = fct_rev(Data), fill = Data)) +
-  geom_tile(color = "white",
+  geom_tile(color = "white", linewidth = 1) +
-            linewidth = 1) + 
   scale_fill_manual(values = splits_pal, guide = "none") +
   theme_minimal() +
-  theme(axis.text.y = element_text(size = rel(2)),
+  theme(
-        axis.text.x = element_blank(),
+    axis.text.y = element_text(size = rel(2)),
-        legend.position = "top",
+    axis.text.x = element_blank(),
-        panel.grid = element_blank()) +
+    legend.position = "top",
+    panel.grid = element_blank()
+  ) +
   coord_equal(ratio = 1) +
   labs(x = NULL, y = NULL)
 all_split
@@ -645,9 +670,18 @@ augment(taxi_fit, new_data = taxi_train) %>%
 augment(taxi_fit, new_data = taxi_train) %>%
   roc_curve(truth = tip, .pred_yes) %>%
   filter(is.finite(.threshold)) %>%
-  pivot_longer(c(specificity, sensitivity), names_to = "statistic", values_to = "value") %>% 
+  pivot_longer(
+    c(specificity, sensitivity),
+    names_to = "statistic",
+    values_to = "value"
+  ) %>%
   rename(`event threshold` = .threshold) %>%
-  ggplot(aes(x = `event threshold`, y = value, col = statistic, group = statistic)) + 
+  ggplot(aes(
+    x = `event threshold`,
+    y = value,
+    col = statistic,
+    group = statistic
+  )) +
   geom_line() +
   scale_color_brewer(palette = "Dark2") +
   labs(y = NULL) +
@@ -1010,34 +1044,39 @@ collect_metrics(final_fit)
 
 ```{r}
 require(tidyverse)
-sitedf <- readr::read_csv("https://www.epa.gov/sites/default/files/2014-01/nla2007_sampledlakeinformation_20091113.csv") |>
+sitedf <- readr::read_csv(
-  select(SITE_ID,
+  "https://www.epa.gov/sites/default/files/2014-01/nla2007_sampledlakeinformation_20091113.csv"
+) |>
+  select(
+    SITE_ID,
     lon = LON_DD,
     lat = LAT_DD,
     name = LAKENAME,
     area = LAKEAREA,
     zmax = DEPTHMAX
-    ) |>
+  ) |>
   group_by(SITE_ID) |>
-  summarize(lon = mean(lon, na.rm = TRUE),
+  summarize(
+    lon = mean(lon, na.rm = TRUE),
     lat = mean(lat, na.rm = TRUE),
     name = unique(name),
     area = mean(area, na.rm = TRUE),
-    zmax = mean(zmax, na.rm = TRUE))
+    zmax = mean(zmax, na.rm = TRUE)
+  )
 
 
-visitdf <- readr::read_csv("https://www.epa.gov/sites/default/files/2013-09/nla2007_profile_20091008.csv") |>
+visitdf <- readr::read_csv(
-  select(SITE_ID,
+  "https://www.epa.gov/sites/default/files/2013-09/nla2007_profile_20091008.csv"
-    date = DATE_PROFILE,
+) |>
-    year = YEAR,
+  select(SITE_ID, date = DATE_PROFILE, year = YEAR, visit = VISIT_NO) |>
-    visit = VISIT_NO
-  ) |>
   distinct()
 
 
-
+waterchemdf <- readr::read_csv(
-waterchemdf <- readr::read_csv("https://www.epa.gov/sites/default/files/2013-09/nla2007_profile_20091008.csv") |>
+  "https://www.epa.gov/sites/default/files/2013-09/nla2007_profile_20091008.csv"
-  select(SITE_ID,
+) |>
+  select(
+    SITE_ID,
     date = DATE_PROFILE,
     depth = DEPTH,
     temp = TEMP_FIELD,
@@ -1046,38 +1085,43 @@ waterchemdf <- readr::read_csv("https://www.epa.gov/sites/default/files/2013-09/
     cond = COND_FIELD,
   )
 
-sddf <- readr::read_csv("https://www.epa.gov/sites/default/files/2014-10/nla2007_secchi_20091008.csv") |>
+sddf <- readr::read_csv(
-  select(SITE_ID, 
+  "https://www.epa.gov/sites/default/files/2014-10/nla2007_secchi_20091008.csv"
+) |>
+  select(
+    SITE_ID,
     date = DATE_SECCHI,
     sd = SECMEAN,
     clear_to_bottom = CLEAR_TO_BOTTOM
   )
 
-trophicdf <- readr::read_csv("https://www.epa.gov/sites/default/files/2014-10/nla2007_trophic_conditionestimate_20091123.csv") |>
+trophicdf <- readr::read_csv(
-  select(SITE_ID,
+  "https://www.epa.gov/sites/default/files/2014-10/nla2007_trophic_conditionestimate_20091123.csv"
-    visit = VISIT_NO,
+) |>
-    tp = PTL,
+  select(SITE_ID, visit = VISIT_NO, tp = PTL, tn = NTL, chla = CHLA) |>
-    tn = NTL,
-    chla = CHLA) |>
   left_join(visitdf, by = c("SITE_ID", "visit")) |>
   select(-year, -visit) |>
   group_by(SITE_ID, date) |>
-  summarize(tp = mean(tp, na.rm = TRUE),
+  summarize(
+    tp = mean(tp, na.rm = TRUE),
     tn = mean(tn, na.rm = TRUE),
     chla = mean(chla, na.rm = TRUE)
   )
 
 
-
+phytodf <- readr::read_csv(
-phytodf <- readr::read_csv("https://www.epa.gov/sites/default/files/2014-10/nla2007_phytoplankton_softalgaecount_20091023.csv") |>
+  "https://www.epa.gov/sites/default/files/2014-10/nla2007_phytoplankton_softalgaecount_20091023.csv"
-  select(SITE_ID,
+) |>
+  select(
+    SITE_ID,
     date = DATEPHYT,
     depth = SAMPLE_DEPTH,
     phyta = DIVISION,
     genus = GENUS,
     species = SPECIES,
     tax = TAXANAME,
-    abund = ABUND) |>
+    abund = ABUND
+  ) |>
   mutate(phyta = gsub(" .*$", "", phyta)) |>
   filter(!is.na(genus)) |>
   group_by(SITE_ID, date, depth, phyta, genus) |>
@@ -1088,7 +1132,7 @@ envdf <- waterchemdf |>
   filter(depth < 2) |>
   select(-depth) |>
   group_by(SITE_ID, date) |>
-  summarise_all(~mean(., na.rm = TRUE)) |>
+  summarise_all(~ mean(., na.rm = TRUE)) |>
   ungroup() |>
   left_join(sddf, by = c("SITE_ID", "date")) |>
   left_join(trophicdf, by = c("SITE_ID", "date"))
@@ -1097,19 +1141,21 @@ nla <- envdf |>
   left_join(phytodf) |>
   left_join(sitedf, by = "SITE_ID") |>
   filter(!purrr::map_lgl(phytodf, is.null)) |>
-  mutate(cyanophyta = purrr::map(phytodf, ~ .x |>
+  mutate(
-    dplyr::filter(phyta == "Cyanophyta") |>
+    cyanophyta = purrr::map(
-    summarize(cyanophyta = sum(abund, na.rm = TRUE))
+      phytodf,
-  )) |>
+      ~ .x |>
+        dplyr::filter(phyta == "Cyanophyta") |>
+        summarize(cyanophyta = sum(abund, na.rm = TRUE))
+    )
+  ) |>
   unnest(cyanophyta) |>
   select(-phyta) |>
   mutate(clear_to_bottom = ifelse(is.na(clear_to_bottom), TRUE, FALSE))
 
-
 # library(rmdify)
 # library(dwfun)
 # dwfun::init()
-
 ```
 
 
@@ -1127,18 +1173,20 @@ skimr::skim(nla)
 nla |>
   filter(tp > 1) |>
   ggplot(aes(tn, tp)) +
-geom_point() +
+  geom_point() +
-geom_smooth(method = "lm") +
+  geom_smooth(method = "lm") +
-scale_x_log10(breaks = scales::trans_breaks("log10", function(x) 10^x),
+  scale_x_log10(
-               labels = scales::trans_format("log10", scales::math_format(10^.x))) +
+    breaks = scales::trans_breaks("log10", function(x) 10^x),
-scale_y_log10(breaks = scales::trans_breaks("log10", function(x) 10^x),
+    labels = scales::trans_format("log10", scales::math_format(10^.x))
-               labels = scales::trans_format("log10", scales::math_format(10^.x)))
+  ) +
+  scale_y_log10(
+    breaks = scales::trans_breaks("log10", function(x) 10^x),
+    labels = scales::trans_format("log10", scales::math_format(10^.x))
+  )
 
 m1 <- lm(log10(tp) ~ log10(tn), data = nla)
 
 summary(m1)
-
-
 ```
 
 ## 复杂指标
@@ -1147,18 +1195,20 @@ summary(m1)
 nla |>
   filter(tp > 1) |>
   ggplot(aes(tp, cyanophyta)) +
-geom_point() +
+  geom_point() +
-geom_smooth(method = "lm") +
+  geom_smooth(method = "lm") +
-scale_x_log10(breaks = scales::trans_breaks("log10", function(x) 10^x),
+  scale_x_log10(
-               labels = scales::trans_format("log10", scales::math_format(10^.x))) +
+    breaks = scales::trans_breaks("log10", function(x) 10^x),
-scale_y_log10(breaks = scales::trans_breaks("log10", function(x) 10^x),
+    labels = scales::trans_format("log10", scales::math_format(10^.x))
-               labels = scales::trans_format("log10", scales::math_format(10^.x)))
+  ) +
+  scale_y_log10(
+    breaks = scales::trans_breaks("log10", function(x) 10^x),
+    labels = scales::trans_format("log10", scales::math_format(10^.x))
+  )
 
 m2 <- lm(log10(cyanophyta) ~ log10(tp), data = nla)
 
 summary(m2)
-
-
 ```
 
 
@@ -1170,13 +1220,14 @@ summary(m2)
 (nla_split <- rsample::initial_split(nla, prop = 0.7, strata = zmax))
 (nla_train <- training(nla_split))
 (nla_test <- testing(nla_split))
-
 ```
 
 ## tidymodels - recipe
 
 ```{r}
-nla_formula <- as.formula("cyanophyta ~ temp + do + ph + cond + sd + tp + tn + chla + clear_to_bottom")
+nla_formula <- as.formula(
+  "cyanophyta ~ temp + do + ph + cond + sd + tp + tn + chla + clear_to_bottom"
+)
 # nla_formula <- as.formula("cyanophyta ~ temp + do + ph + cond + sd + tp + tn")
 nla_recipe <- recipes::recipe(nla_formula, data = nla_train) |>
   recipes::step_string2factor(all_nominal()) |>
@@ -1191,9 +1242,9 @@ nla_recipe
 
 ```{r}
 nla_cv <- recipes::bake(
-    nla_recipe, 
+  nla_recipe,
-    new_data = training(nla_split)
+  new_data = training(nla_split)
-  ) |>
+) |>
   rsample::vfold_cv(v = 10)
 nla_cv
 ```
@@ -1260,7 +1311,7 @@ if (FALSE) {
     metrics = yardstick::metric_set(rmse, rsq, mae),
     control = tune::control_grid(verbose = TRUE)
   )
-saveRDS(xgboost_tuned, "./xgboost_tuned.RDS")
+  saveRDS(xgboost_tuned, "./xgboost_tuned.RDS")
 }
 xgboost_tuned <- readRDS("./xgboost_tuned.RDS")
 ```
@@ -1298,7 +1349,7 @@ xgboost_tuned |>
 
 ```{r}
 xgboost_best_params <- xgboost_tuned |>
-  tune::select_best("rmse")
+  tune::select_best(metric = "rmse")
 
 knitr::kable(xgboost_best_params)
 ```
@@ -1327,18 +1378,19 @@ train_prediction <- xgboost_model_final |>
   # fit the model on all the training data
   fit(
     formula = nla_formula,
-    data    = train_processed
+    data = train_processed
   ) |>
   # predict the sale prices for the training data
   predict(new_data = train_processed) |>
-  bind_cols(nla_train |>
+  bind_cols(
-  mutate(.obs = log10(cyanophyta)))
+    nla_train |>
+      mutate(.obs = log10(cyanophyta))
+  )
 xgboost_score_train <-
   train_prediction |>
   yardstick::metrics(.obs, .pred) |>
   mutate(.estimate = format(round(.estimate, 2), big.mark = ","))
 knitr::kable(xgboost_score_train)
-
 ```
 
 ## tidymodels - train evaluation
@@ -1349,10 +1401,8 @@ knitr::kable(xgboost_score_train)
 #| out-width: "80%"
 train_prediction |>
   ggplot(aes(.pred, .obs)) +
-geom_point() +
+  geom_point() +
-geom_smooth(method = "lm")
+  geom_smooth(method = "lm")
-
-
 ```
 
 
@@ -1360,18 +1410,20 @@ geom_smooth(method = "lm")
 
 
 ```{r}
-test_processed  <- bake(nla_recipe, new_data = nla_test)
+test_processed <- bake(nla_recipe, new_data = nla_test)
 
 test_prediction <- xgboost_model_final |>
   # fit the model on all the training data
   fit(
     formula = nla_formula,
-    data    = train_processed
+    data = train_processed
   ) |>
   # use the training model fit to predict the test data
   predict(new_data = test_processed) |>
-  bind_cols(nla_test |>
+  bind_cols(
-  mutate(.obs = log10(cyanophyta)))
+    nla_test |>
+      mutate(.obs = log10(cyanophyta))
+  )
 
 # measure the accuracy of our model using `yardstick`
 xgboost_score <- test_prediction |>
@@ -1394,7 +1446,7 @@ cyanophyta_prediction_residual <- test_prediction |>
   select(.pred, residual_pct)
 
 cyanophyta_prediction_residual |>
-ggplot(aes(x = .pred, y = residual_pct)) +
+  ggplot(aes(x = .pred, y = residual_pct)) +
   geom_point() +
   xlab("Predicted Cyanophyta") +
   ylab("Residual (%)")
@@ -1411,9 +1463,8 @@ ggplot(aes(x = .pred, y = residual_pct)) +
 #| out-width: "80%"
 test_prediction |>
   ggplot(aes(.pred, .obs)) +
-geom_point() +
+  geom_point() +
-geom_smooth(method = "lm", colour = "black")
+  geom_smooth(method = "lm", colour = "black")
-
 ```
 
 
@@ -1421,5 +1472,4 @@ geom_smooth(method = "lm", colour = "black")
 ## 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 = "https://drc.drwater.net/course/public/RWEP/PUB/SD/")`
-