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69th Tokyo.R @kilometer BeginneR Session 1 -- Data Import / Export -- 2018.04.21 at Roppongi

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Who！？

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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(霊長類) 脳イメージング 医療システム工学 R歴： ~ 10年ぐらい 流行: ラム肉

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BeginneR Session

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BeginneR

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BeginneR Advanced Hoxo_m If I have seen further it is by standing on the sholders of Giants. -- Sir Isaac Newton, 1676

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BeginneR

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Before After BeginneR Session BeginneR BeginneR

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Input Output Today’s talk ? ? Table data Image data Other formats Introduction Summary

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を、始めたいんだけど。 私もそろそろ ぱそこん できるんでしょ？教えてよ。 ぱそこん いいけど、 で何がしたいの？ ぱそこん って何でもできるんでしょ？ でも、どうしたらいいか分かんないんだ。 一昔前

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を、始めたいんだけど。 私もそろそろ じんこう ちのー できるんでしょ？教えてよ。 いいけど、 で何がしたいの？ って何でもできるんでしょ？ でも、どうしたらいいか分かんないんだ。 最近 じんこう ちのー じんこう ちのー

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を、始めたいんだけど。 私もそろそろ できるんでしょ？教えてよ。 いいけど、 で何がしたいの？ って何でもできるんでしょ？ でも、どうしたらいいか分かんないんだ。

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を、始めたいんだけど。 私もそろそろ できるんでしょ？教えてよ。 いいけど、 で何がしたいの？ って何でもできるんでしょ？ でも、どうしたらいいか分かんないんだ。

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Input Output Do NOT start from here

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Input Output Do NOT start from here Whatever …

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Input Output Do NOT start from here Whatever … 1 2 3

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Input Output Today’s talk ? ?

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Integrated Development Environment RStudio https://www.rstudio.com/

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Integrated Development Environment RStudio https://www.rstudio.com/

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RStudio

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Projects RStudio

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RStudio > Project 一説には2147483647個存在するとも言われるRStudioの利 点のなかでも、 ・Rなどのソースファイルをタブで並べて表示できる ・そのタブの順番を保持できる ・タブの内容をファイルを保存せずにRStudioを終了して しまっても、編集途中の内容を保持してくれている 等が全国2147483647人のRユーザーのQOLを大いに向上さ せたのは、おそらく異論がないことと思われます。 34UVEJPͬͯͳΜͩʁ 1SPKFDUͬͯͳΜͩ !XBLVUFLB https://qiita.com/wakuteka/items/9599bb0a8985d98928d7

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File > New Project… > New Directory > New Project hogehoge

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hogehoge ~/Documents/R hogehoge.Rproj .Rproj.user Project Root Directory Double click!! .RData .Rhistory Auto saved project information Open project New!!

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~/Documents/R project1 project2 project3 project4

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Input Output Today’s talk ? ? Table data Image data Other formats Summary Introduction

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Table format data Table data Image data Other formats Introduction Summary

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x <- read.table("import.txt") Import Table format data object assignment operator file path function

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x <- read.table("import.txt") Import Table format data object assignment operator file path function

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~/Documents/ import.txt Target!! data x <- read.table("~/Documents/data/import.txt") setwd("~/Documents/data/") x <- read.table("import.txt") 1. set working directory 2. then use relative path Method②: use absolute path Method ① Import Table format data

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x <- read.table("~/Documents/data/import.txt") setwd("~/Documents/data/") x <- read.table("import.txt") Method②: use absolute path Method ①: setwd – relative path # working directory wd <- c("~/Documents/data/") # make full path: bind characters path <- paste0(wd, "import.txt") # import data x <- read.table(path) or

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prj ~/Documents/R prj.Rproj import.txt Default working directory (project root) Target!! x <- read.table("import.txt") can use relative path without setwd

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x <- read.table(file) Import Table format data

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x <- read.table(file) Import Table format data you

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Table format data Comma-separated values (.csv) Tab-separated values (.tsv) Space-SV Semicolon-SV … Delimiter-separated values

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Table format data x = np.genfromtxt("hoge.csv", delimiter=",") x <- read.table("hoge.csv", sep=",") Optional argument(s)

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?read.table Usage read.table(file, header = FALSE, sep = "", quote = "∖", dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"), row.names, col.names, as.is = !stringsAsFactors, na.strings = "NA", colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = "#", allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors(), fileEncoding = "", encoding = "unknown", text, skipNul = FALSE) Import Table format data

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?read.table Usage read.table(file, header = FALSE, sep = "", quote = "∖", dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"), row.names, col.names, as.is = !stringsAsFactors, na.strings = "NA", colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = "#", allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors(), fileEncoding = "", encoding = "unknown", text, skipNul = FALSE) Import Table format data You must specify If not specified, applied this default value Optional argument(s) 引数 "file" がありませんし、省略時既定値もありません If not,

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?read.table Usage read.table(file, header = FALSE, sep = "", quote = "∖", dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"), row.names, col.names, as.is = !stringsAsFactors, na.strings = "NA", colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = "#", allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors(), fileEncoding = "", encoding = "unknown", text, skipNul = FALSE) Import Table format data

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?read.table Usage read.table(file, skip = 0, header = FALSE, nrows = -1, row.names, fileEncoding = "") Import Table format data

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cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html > x sex height weight 1 F 158 51 2 F 162 55 3 M 177 72 4 M 173 57 5 M 166 64 Import Table format data

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data # 先頭_行は読み込まない # カラム名の行が存在する # 行名のカラム名/番号を指定 # データ部分の行数

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x <- read.table( "import.txt", skip = 1, header = TRUE, row.names = "data", nrows = 5, fileEncoding = "UTF8") cf. R-Tips: 40. ファイルからデータを読み込む http://cse.naro.affrc.go.jp/takezawa/r-tips/r/40.html Import Table format data # 先頭_行は読み込まない # カラム名の行が存在する # 行名のカラム名/番号を指定 # データ部分の行数

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第67回 初心者セッション1 @y__mattu https://github.com/ymattu/TokyoR67 Import Table format data

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x <- read.table("import.csv", header = T, sep = "," quote = "∖", dec = ".") x <- read.csv("import.csv") Import Table format data Wrap

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x <- read.table(file) Import Table format data you Wrappers

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x <- read.table(file) Import Table format data you

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Package … {utils} Package {base} Package

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Package Package Package Package Package Package Package Package Package Package Package Package Package Package Package

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packages you

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cf. http://rpkg.gepuro.net/ cf. https://cran.r-project.org/web/packages/ at 2018.02.20

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Package Default pkgs Package Package Package CRAN Guithub Package Package Package Package Package Package Package Package install.packages githubinstall

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utils::read.table(file) Import Table format data Default installed pkg (optional) Function data.table::fread(file) Install REQUIRED

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Import Table format data List of installed packages

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Import Table format data data.table::fread (file) Installation (from CRAN) install.packages("data.table") Usage library("data.table") fread (file) or

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Import Table format data library("data.table") > sessionInfo() ... other attached packages: [1] data.table_1.10.4-3 Global environment # Attach {data.table}

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Import Table format data library("data.table") fread (file, data.table = FALSE) Fast!!! Flexible!!! Need installation Should specify: data.table =FALSE Automatic!!! Simple!!!

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write.table(x, "export.txt") write.csv(x, "export.csv") object file path Export Table format data Wrapper

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Input Output Today’s talk ? ? Table data Image data Other formats Summary Introduction

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Image data Table data Image data Other formats Summary Introduction

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Export image data ?

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Export image data Use Graphic Device ready graphic device close graphic device draw graph(s) plotting functions ・High-level ・Low-level ・Interactive Basic Graphics in R http://bcb.dfci.harvard.edu/~aedin/courses/BiocDec2011/2.Plotting.pdf

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Export image data Use Graphic Device ready close draw png("hoge.png") plot(iris) dev.off() High-level plotting function

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hogehoge ~/Documents/R hogehoge.Rproj hoge.png New!!

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Export image data Graphic Devices in {grDevices} > help(device) pdf png jpeg tiff bmp ... Write PDF graphics commands to a file PNG bitmap device JPEG bitmap device TIFF bitmap device BMP bitmap device

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Export image data Graphic Devices in {grDevices} pdf png jpeg tiff bmp svg cairo_pdf cairo_ps Scalable vector graphics Cairographics based PDF Cairographics based PostScript

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Export plot ready graphic device close graphic device draw graph(s) Image data processing Import & Export image x <- read***( ) write***(x, ) processing

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png::readPNG Import image data tiff::readTIFF jpeg::readJPEG bmp::read.bmp

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png::readPNG Import image data tiff::readTIFF jpeg::readJPEG bmp::read.bmp

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png::readPNG Import image data tiff::readTIFF jpeg::readJPEG bmp::read.bmp EBImage::readImage magick::image_read imager::load.image OpenImageR::readImage biOps::readJpeg

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png::readPNG Import image data tiff::readTIFF jpeg::readJPEG bmp::read.bmp EBImage::readImage magick::image_read imager::load.image OpenImageR::readImage biOps::readJpeg

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Import image data EBImage::readImage magick::image_read Export image data EBImage::writeImage # not CRAN pkg magick::image_write # low googlability

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Import image data EBImage::readImage magick::image_read Export image data EBImage::writeImage # not CRAN pkg magick::image_write # low googlability

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Salvador Dalí 1904-1989 profile of time wikipedia

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http://seekr.jp/

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Input Output Today’s talk ? ? Table data Image data Other formats Summary Introduction

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Table data Image data Other formats Other formats Summary Introduction

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.xls or .xlsx readxl::read_excel( file, GJMFQBUI sheet = 1) TIFFUOBNFPS/P

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.json jsonlite::read_json(file) jsonlite::write_json(file) Wrap from_json(file, simplifyVector =T) Wrap to_json(obj, file, simplifyVector =T)

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tuneR::readMP3(file) .wav or .mp3 tuneR::readWave(file) tuneR::writeWave(object, file)

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.sas or .dta or .sav SAS Stata SPSS haven::read_sas("hoge.sas7bdat") haven::read_dta("hoge.dta") haven::read_sav("hoge.sav")

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Summary Table data Image data Other formats Summary Introduction

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Input Output Do NOT start from here Whatever … 1 2 3

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Data Import / Export ? ?

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packages you

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Data Import / Export ? ? {readxl} {data.table} {EBImage} {magick} {jsonlite} {tuneR} {haven} {grDevices} {utils} packages

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~/Documents/R project1 project2 project3 project4

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Before After BeginneR Session BeginneR BeginneR ?

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BeginneR Advanced Hoxo_m If I have seen further it is by standing on the sholders of Giants. -- Sir Isaac Newton, 1676

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Enjoy!! KMT˝

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Bar DraDra KMT˝