2021-07-19

植物学和生态学的一些R语言学习资源

软件

R：https://www.r-project.org
Rstudio： https://www.rstudio.com
VScode： https://code.visualstudio.com
git - 简易指南 https://rogerdudler.github.io/git-guide/index.zh.html
tinytex: https://yihui.org/tinytex/
Miktex: https://miktex.org

程序包

The learnr package Interactive Tutorials for R https://rstudio.github.io/learnr/
Yu Guangchuang ggtree https://guangchuangyu.github.io/software/ggtree/
谢益辉等 Rmarkdown https://rmarkdown.rstudio.com/
谢益辉等 blogdown https://bookdown.org/yihui/blogdown/
谢益辉等 pagedown https://github.com/rstudio/pagedown
sf 程序包 https://r-spatial.github.io/sf/
CRAN Task Views: https://cran.r-project.org/web/views/ 程序包分类列表
awesome-R https://github.com/qinwf/awesome-R
Roxana Noelia Villafañe Learning R - Resources https://github.com/data-datum/learning_R
Karthik Ram, Scott Chamberlain, and Carl Boettiger et. al. ropensci https://ropensci.org/packages/

图书

李东风 R 语言教程 https://www.math.pku.edu.cn/teachers/lidf/docs/Rbook/html/_Rbook/Rbook.pdf
王敏杰 数据科学中的R语言 ： https://bookdown.org/wangminjie/R4DS/ 课程录像 https://www.bilibili.com/video/BV1VE411N765/
Jenny Bryan Data wrangling, exploration, and analysis with R https://stat545.com/
Winston Chang R Graphics Cookbook, 2nd edition https://r-graphics.org/ 主要介绍ggplot2的用法
Daniel Borcard, François Gillet and Pierre Legendre Numerical Ecology with R, second edition http://adn.biol.umontreal.ca/~numericalecology/numecolR/ 数量生态学在R中的实现，赖江山博士翻译过中文版。
Emmanuel Paradis Analysis of Phylogenetics and Evolution with R https://www.springer.com/gp/book/9781461417422 进化分析必读
Emmanuel Paradis Population Genomics with R 1st Edition https://www.amazon.com/Population-Genomics-R-Emmanuel-Paradis/dp/1138608181 群体基因组学必读
Robin Lovelace, Jakub Nowosad and Jannes Muenchow Geocomputation with R https://geocompr.robinlovelace.net/ 空间分析和地图绘制
Roger D. Peng (2020) R programming for data sciences (https://bookdown.org/rdpeng/rprogdatascience/)
Wickham, H R for data science (https://r4ds.had.co.nz/)
Claus O. Wilke Fundamentals of Data Visualization (https://clauswilke.com/dataviz/)
Jack Taylor Data Skills for Reproducible Science https://psyteachr.github.io/msc-data-skills/
Hadley Wickham The tidyverse style guide https://style.tidyverse.org/
Danielle Navarro Learning statistics with R https://github.com/djnavarro/rbook https://tidylsr.djnavarro.net/
Edzer Pebesma, Roger Bivand Spatial Data Science with applications in R https://keen-swartz-3146c4.netlify.app/ 空间分析经典
Robert Tibshirani, Jerome Friedman, The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Second Edition https://web.stanford.edu/~hastie/ElemStatLearn/ 机器学习经典
James, G., Witten, D., Hastie, T., & Tibshirani, R. (2013). An introduction to statistical learning. New York: springer. (https://www.statlearning.com/) 机器学习最好的入门图书之一
Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017). Habitat suitability and distribution models: with applications in R. Cambridge University Press. code: https://github.com/vdicolab/hsdm R语言物种分布模型入门
Gotelli, N. J., & Ellison, A. M. (2004). A primer of ecological statistics (Vol. 1). Sunderland: Sinauer Associates. 生态学数据分析经典入门
Michael Whitlock and Dolph Schluter The Analysis of Biological Data https://whitlockschluter3e.zoology.ubc.ca/ UBC的生物学数据分析
Altuna Akalin Computational Genomics with R https://compgenomr.github.io/book/ 计算基因组学
张敬信 R语言编程–基于tidyverse (https://github.com/zhjx19/introR)
邓飞 R语言进阶笔记 (https://dengfei2013.gitee.io/r-language-advanced/)
Xie Yihui bookdown: Authoring Books and Technical Documents with R Markdown https://bookdown.org/yihui/bookdown/ 用Rmarkdown写书
Xie Yihui, Christophe Dervieux, Emily Riederer R Markdown Cookbook https://bookdown.org/yihui/rmarkdown-cookbook/ Rmarkdown秘籍
Xie Yihui, Amber Thomas, Alison Presmanes Hill blogdown: Creating Websites with R Markdown https://bookdown.org/yihui/blogdown/ 用Rmarkdown写博客

课程

University of Massachusetts Boston Bio607 生物统计课程 Biol 607: Intro to Computational Data Analysis for Biology (https://biol607.github.io/)
Geography 503: GEO Spatial Data Science https://github.com/AdamWilsonLabEDU/GEO511 空间分析
Walter Jetz, Erica Stuber, Cory Merow, Scott Rinnan, Brett Jesmer, Gabriel Reygondeau, Ruth Oliver (2019) EEB 713, Spring 2019: Concepts and methods in global biodiversity change research in the age of big data https://cmerow.github.io/YaleBGCCourses/ https://github.com/cmerow/RDataScience 耶鲁大学的大数据与生态学课程
François Michonneau and Auriel Fournier Data Analysis and Visualization in R for Ecologists https://datacarpentry.org/R-ecology-lesson/ 为广泛采用的DataCarpentry的课程材料
David Zelený Analysis of community ecology data in R https://www.davidzeleny.net/anadat-r/doku.php/en:start 群落数据分析
Jenny Bryan, the STAT 545 TAs, Jim Hester Happy Git and GitHub for the useR https://happygitwithr.com/ 学习使用git和github
R for Reproducible Scientific Analysis http://swcarpentry.github.io/r-novice-gapminder/
DATA SCIENCE FOR ECOLOGISTS AND ENVIRONMENTAL SCIENTISTS (https://ourcodingclub.github.io/course.html)

操作指南

Karl Broman R package primer a minimal tutorial https://kbroman.org/pkg_primer/ 编写R程序包
Robert J. Hijmans and Jane Elith Species distribution modeling https://rspatial.org/raster/sdm/index.html dismo、raster、terra等程序包的作者Robert Hijmans写的空间分析材料

快速参考

R Studio Cheatsheets: https://www.rstudio.com/resources/cheatsheets/

网站

统计之都： https://cosx.org/
Hadley Wickham的个人网站，介绍tidyverse: http://hadley.nz/
谢益辉的个人网站: https://yihui.org/
Karl Broman的个人网站：https://kbroman.org/talks.html
Robin Lovelace的个人网站： https://www.robinlovelace.net/
Adam B. Smith 的个人网站 https://github.com/adamlilith

视频

R语言编程 https://www.bilibili.com/video/BV1D7411T77Z?from=search&seid=1630947937465437556
YOUTUBE R语言编程合集: https://pan.baidu.com/s/1_wyj1sTeb7wp4cWFwk6Vzw 提取码：6pfj

其他

英国生态学会 Guides to Better Science指南系列 https://www.britishecologicalsociety.org/publications/guides-to/

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