TokyoR#102_RMarkdown - Speaker Deck

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#102 @kilometer00 2022.10.22 R Markdown for beginners

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Who！？名前：三村 @kilometer 職業：ポスドク (こうがくはくし) 専⾨：⾏動神経科学(霊⻑類) 脳イメージング医療システム⼯学 R歴： ~ 10年ぐらい流⾏: 南極探検隊

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宣伝!! （書籍の翻訳に参加しました。）第五刷！！

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BeginneR Session

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BeginneR

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Beginne R Advance d Hoxo_m If I have seen further it is by standing on the shoulders of Giants. -- Sir Isaac Newton, 1676

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Before A'er BeginneR Session BeginneR BeginneR

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"a" != "b" # is A in B? ブール演算⼦ Boolean Algebra [1] TRUE 1 %in% 10:100 # is A in B? [1] FALSE

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George Boole 1815 - 1864 A Class-Room Introduc2on to Logic h7ps://niyamaklogic.wordpress.com/c ategory/laws-of-thoughts/ Mathematician Philosopher &

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ブール演算⼦ Boolean Algebra A == B A != B George Boole 1815 - 1864 A | B A & B A %in% B # equal to # not equal to # or # and # is A in B? wikipedia

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Programing

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AI Programmer !? import sample data scatter plot speed and dist as x and y axes, respectively import pandas as pd import matplotlib.pyplot as plt data = pd.read_csv('sample_data.csv') plt.scatter(data['speed'], data['dist’]) plt.show() library(tidyverse) df <- read_csv("sample_data.csv") df %>% ggplot(aes(x = speed, y = dist)) + geom_point() https://aiprogrammer.hashlab.jp/

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Programing Write Run Read Think Write Run Read Think Communicate Share

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#102 @kilometer00 2022.10.22 R Markdown for beginners

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Program documentation code # comment Input Output document (for PC) (for human)

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Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to humans what we want the computer to do. — Donald E. Knuth, Literate Programming, 1984 プログラム構築に関する伝統的な態度を切り替えてみましょう。コンピュータに何をするべきかを指図するのが主な仕事だと考えるのではなく、むしろコンピュータに何をして欲しいかを⼈間に説明することに集中しよう。 — ドナルド・E・クヌース, ⽂芸的プログラミング, 1984 Literate Programming

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Literate Programming code document # comment Input Output

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Literate Programming in R Sweave knitr rmarkdown Quato? 2012 2002 2014 WAB → Noweb ↓ 2021 R Markdown: The Definitive Guide Yihui Xie, J. J. Allaire, Garrett Grolemund, 2022 https://bookdown.org/yihui/rmarkdown/#ref-xie2015 Yihui Xie @xieyihui

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R Markdown ① Make a new .Rmd file ② Write something (for human) ③ Knit it!!

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R Markdown ① Make a new .Rmd file ② Write something (for human) using markdown & R ③ Knit it!!

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Markdown A simple markup language that uses plain text formatting syntax plain text with markdown .html .pdf .docx

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Markup Language Plain text Rich text HTML = Hyper Text Markup Language Web browser

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Markup Language Plain text Rich text Markdown HTML

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Markup Language Plain text Rich text Markdown HTML Pandoc pandoc -f markdown -t html hoge.md > hoge.html

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Markdown Plain text Rich text *This* This **This** This ***This*** ~~This~~ This This This This

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Markdown Plain text Rich text

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Markdown Plain text Rich text

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Markdown Plain text Rich text

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```r library(palmerpenguins) penguins[1, ] ``` ``` # A tibble: 1 × 8 species island bill_…¹ bill_…² flipp…³ body_…⁴ sex year 1 Adelie Torger… 39.1 18.7 181 3750 male 2007 # … with abbreviated variable names ¹bill_length_mm, # ²bill_depth_mm, ³flipper_length_mm, ⁴body_mass_g ``` Markdown Plain text Rich text

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Write .md .md .r write code test code write document copy code paste code copy results paste results write document write document

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r

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.Rmd .md .html .pdf .docx knitr Pandoc

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r Peaceful world ・No copy & paste ・No window switching

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r Peaceful world ・No copy & paste ・No window switching You MUST write docs about the R code You JUST write docs about your analysis with R code

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r --- title: "Hoge" output: html_document: default --- YAML header (YAML Ain't a Markup Language.)

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r --- title: "Hoge" output: html_document: keep_md: TRUE --- YAML header (YAML Ain't a Markup Language.)

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Knit .Rmd in English .Rmd → .html .Rmd → .pdf .Rmd → .docx Easy!! Great!! Comfortable! Good!! Okay, if you need.

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Knit .Rmd in Japanese .Rmd → .html .Rmd → .pdf .Rmd → .docx Easy!! Great!! Darkness Darknes(

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As soon as Anakin came before him on Coruscant, Yoda could sense darkness in his soul. --- The Phantom Menace

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r YAML header for Japanese PDF (in my env.) --- title: "segments" output: pdf_document: latex_engine: xelatex documentclass: bxjsarticle classoption: xelatex,ja=standard mainfont: Hiragino Kaku Gothic Pro ---

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r Code Chunk 1 Code Chunk 2 ```{r, chunk1} ``` ```{r, chunk2} Chunk name

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Chunk options ```{r chunk1, ...} ``` Language Name Options echo eval include results fig.width / fig.height collapse warning message

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Chunk options ```{r chunk1, options...} ``` ```{r} #| chunk1 #| options... ``` =

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r ```{r setup, include=FALSE} knitr::opts_chunk$set( echo = TRUE ) ``` Global setting of chank options

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Write .Rmd .Rmd set document write document write .r write document write document test .r write .r test .r Code Chunk 1 ```{r, chunk1} ``` Run this chunk: ⌘+Shift+↩

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.Rmd set document write document write .r write document write document test .r write .py test .py ```{r pyenv, include=FALSE} reticulate::use_python( python = ".../bin/python", required = TRUE ) ``` Write python in .Rmd

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Write python in .Rmd

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Write python in .Rmd https://speakerdeck.com/kilometer

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In summary ...

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R Markdown ① Make a new .Rmd file ② Write something (for human) using markdown & R ③ Knit it!!

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.Rmd .md .html .pdf .docx knitr Pandoc

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Chunk options ```{r chunk1, ...} ``` Language Name Options echo eval include results fig.width / fig.height collapse warning message