rmarkdown楽しい！：研究の再現性のために/NagoyaR16

研究の透明性と再現性を確保するために，Rのコードと分析結果をRMarkdownを使ってドキュメンテーションする方法を紹介します。

Transcript

1. rmarkdownָ͍͠ʂ
   —ݚڀͷ࠶ݱੑͷͨΊʹ—
   2016.07.23 Nagoya.R #16
   ໊ݹ԰େֶେֶӃࠃࡍ։ൃݚڀՊ D3 ాଜ༞
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2. ֓ཁ
   • ର৅
   • RͰॻ͍ͨίʔυ΍ͦͷ݁ՌΛอଘͨ͠ΓγΣΞ͠
   ͨΓ͍ͨ͠ํʢ૝ఆ͍ͯ͠Δͷ͸ओʹݚڀ໨తʣ
   • ಺༰
   • Nagoya.R #14ͷʮςΩετΤσΟλΛ࢖͓͏ʯͷ্
   Ґޓ׵൛ʢhttps://speakerdeck.com/tam07pb915/
   nagoyar15ʣ
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3. ͓அΓ
   • RStudioલఏͷ࿩ʹͳΓ·͢
   • RStudio࢖ͬͨ΄͏͕͍͍Ͱ͢ʢ࢖Θͳ͍ཧ༝͕
   ͋·Γͳ͍ʣ
   • ࢀߟɿSapporoR#6 ॳ৺ऀηογϣϯʢhttp://
   www.slideshare.net/simizu706/sapporor6ʣ
   • ͱ͘ʹϋϯζΦϯతͳ͜ͱ͸͠·ͤΜ
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4. ҰݴͰݴ͏ͱ
   • rmarkdownָ͕͍͠
   • rmarkdownͰ෼ੳίʔυͱ݁ՌΛγΣΞ͠Α͏
   • rmarkdown͕͍͍
   • ͱʹ͔͘rmarkdown͍͢͝
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5. ͜͏͍͏ͷ࡞Γ͔ͨͬͨ
   5
   Murakami (2016)
   

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6. ͜͏͍͏ͷ࡞Γ͔ͨͬͨ
   6
   Mizumoto, Ikeda, & Takeuchi (2016)
   

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7. ͳʹ͜ΕHTMLͰશ෦ॻ
   ͘ͷʁ͑ʁͲ͏͢Δͷʁ
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8. R Markdown
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9. R Markdownͱ͸
   • kazutanઌੜͷࢿྉΛݟ·͠ΐ͏
   9
   https://kazutan.github.io/SappoRoR6/rmd_slide.html#/
   http://kazutan.github.io/KandaiR1/rmd_intro.html#/
   

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10. R Markdownͱ͸
    • RͰ࢖͑Δmarkdownܗࣜͷݴޠ
    • ෼ੳʴυΩϡϝϯτ࡞੒͕؆୯ʹͰ͖Δ
    • ίʔυ+#ίϝϯτΞ΢τΈ͍ͨͳ΋ͷΛ΋ͬͱ៉ྷʹ
    Ͱ͖Δ
    • ਤ΋Ұॹʹग़ྗՄೳʂ
    • ෼ੳʹ࢖ͬͨίʔυͱͦͷ݁ՌΛ·ͱΊͨϑΝΠϧΛ
    ࡞ΕΔ
    10
    

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11. ͳͥR Markdown?
    • ݚڀͷ෼ੳʹRΛ༻͍Δ͜ͱ͕ͲΜͲΜ૿͖͑ͯ
    ͍ͯΔ
    • RΛݚڀʹ༻͍Δେ͖ͳཧ༝͸࠶ݱੑ
    ʢMizumoto & Plosnky, 2016)
    • σʔλͱίʔυ͕͋Ε͹୭Ͱ΋෼ੳ݁ՌΛ࠶ݱ
    Ͱ͖Δ
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12. ͳͥR Markdown?
    • ͨͩ͠…
    • Rͷίʔυ͕ެ։͞ΕΔ͜ͱ΋গͳ͚Ε͹ੜσʔλ
    ͕ެ։͞ΕΔ͜ͱ͸΋ͬͱগͳ͍
    • ࿦จΛಡΜ͚ͩͩͰ͸ɼͲ͏͍͏աఔΛܦͯ෼ੳ
    ͨ͠ͷ͔Θ͔Βͳ͍͜ͱ΋ଟ͍
    • RͷίʔυΛͲΜͲΜެ։͠Α͏ʂ෼ੳͷ݁Ռ΋ؚΊ
    ͯެ։͠Α͏ʂ
    12
    

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13. R Markdown͸Ͳ͏࢖͏ʁ
    • RStudio͕ඞཁʢRStudio։ൃνʔϜ͕
    RMarkdownΛ࡞͍ͬͯΔʣ
    • جຊతͳ࡞ۀ͸νʔτγʔτݟΕ͹Ͱ͖Δʂ
    13
    

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15. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ1
    • File -> New File -> R Markdown ·ͨ͸ࠨ্ͷ
    ΞΠίϯΛΫϦοΫͯ͠R MarkdownΛબ୒
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16. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ2
    • Document, Presentation, Shiny, From Template
    ͷத͔ΒDocumentΛબ୒ʢεϥΠυ࡞Δͱ͖
    ͸Presentationʣ
    • λΠτϧͱ໊લͷೖྗ
    • ग़ྗͷબ୒
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17. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ3
    • ͢ΔͱউखʹϑΝΠϧͷϝλσʔλ৘ใΛ
    YAMLϑΥʔϚοτͰ࡞ͬͯ͘Ε·͢
    • ͜͜Ͱ௚ͯ͠΋OK
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18. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ3
    • ͋ͱ͸markdownܗࣜͰจॻΛॻ͖ͭͭɼνϟ
    ϯΫͱ͍͏۠੾ΓͰίʔυΛॻ͘
    18
    νϟϯΫ։࢝ͷϚʔΫ
    νϟϯΫͷऴΘΓͷϚʔΫ
    

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19. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ3
    • ϑΥʔϚοτ͸νʔτγʔτݟΕ͹Α͍
    • # Header1, ## Header2 etc.
    • > block quote, **bold** etc.
    19
    

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20. R Markdown͸Ͳ͏࢖͏ʁ
    • ```{r }ͷதͰΦϓγϣϯͷࢦఆ΋Մೳ
    • ίʔυ͸ग़ྗ͢Δ͚Ͳ࣮ߦ͸͠ͳ͍
    • ίʔυ͸Ӆͯ݁͠Ռ͚ͩग़ྗ
    • ίʔυ΋݁Ռ΋ग़ྗ͢Δ
    • ܯࠂϝοηʔδ΍ΤϥʔϝοηʔδΛදࣔ͢Δ
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    etc.
    

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21. R Markdown͸Ͳ͏࢖͏ʁ
    • खॱ4
    • R MarkdownͰॻ͍ͨ΋ͷʢ֦ுࢠ.rmdʣΛ
    HTML౳ʹॻ͖ग़͢
    • KnitϘλϯԡ͚ͩ͢
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22. ͓͓͓͓͓͓͓͓͓
    22
    ͜ͷग़ྗ͞Ε͕ͨ࣌ΊͬͪΌؾ
    ͍͍࣋ͪͰ͢ͷͰ͓ࢼ͍ͩ͘͠͞
    

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23. R Markdown͸Ͳ͏࢖͏ʁ
    • ग़ྗܗࣜ͸HTML͕͍͍ʢσϑΥϧτʣ
    • Officeͳͯ͘΋Wordग़ྗՄೳ
    • ͨͩ͠ɼ͋·Γඒ͘͠ͳ͍
    • PDFग़ྗ͸৭ʑ໽հ
    • ೔ຊޠͷจࣈίʔυ
    • Tex؀ڥͰͳ͍ͱͰ͖ͳ͍
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24. ग़ྗͨ͋͠ͱ͸Ͳ͏͢Δʁ
    • ւ֎ͷJournalͳΒ͍͍ͨͯ͸Supplementary FilesΛఏग़͢Δ
    ͜ͱ͕Ͱ͖ΔͷͰɼhtmlϑΝΠϧΛ࿦จͱҰॹʹग़ͤ͹Α͍
    • ࠷ॳʹ঺հͨ͠Murakami (2016)͸͜ͷλΠϓ
    • ࠃ಺ͷJournalͳΒɼϦϯΫΛ࿦จதʹॻ͘
    • ࣗ෼ͷ΢ΣϒαΠτɼresearchmapɼΦϯϥΠϯετϨʔ
    δαʔϏε౳ʑʹΞοϓϩʔυͯ͠ެ։
    • Mizumoto, Ikeda, and Takeuchi (2016)͸͜ͷλΠϓ
    24
    

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25. ͓·͚
    • ݚڀͷ࠶ݱੑҎ֎ͷ໘Ͱ΋ྑ͍ͱ͜Ζ
    • ڞಉݚڀʹ͓͚Δ෼ੳ݁Ռͷڞ༗
    • ෼ੳ݁Ռ͚ͩͰ͸ͳ͘ɼͲͷΑ͏ͳաఔΛܦͯಘΒ
    Εͨ݁Ռͳͷ͔΋ڞ༗͢Δ͜ͱ͸ॏཁ
    • ޙഐɾֶੜͷࢦಋ
    • ࣍ʹಉ͡Α͏ͳ෼ੳΛ͢Δػձ͕͋ͬͨΒͦΕΛݩ
    ʹRͰ෼ੳ͢Ε͹ྑ͍
    25
    

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26. ͓ΘΓʹ
    • ·ͣ͸ɼίϯιʔϧ্Ͱ͸ͳ͘R ScriptϑΝΠϧʹ
    ίʔυΛॻ͘ΫηΛ͚ͭΔʢࣗ෼ࣗ਎͕͋ͱͰ෼
    ੳ΍Γ௚͢ࡍʹ΋ָʣ
    • ࿦จΛॻ͍ͯ౤ߘ͢Δ͜ͱΛ໨ࢦ͢ͳΒɼ࠷ॳ͔
    ΒR MarkdownͰॻ͍͓͍ͯͯଛ͸ͳ͍
    • ͳΜͳΒεϥΠυͩͬͯR MarkdownͰ࡞ΕͪΌ͏
    ͔Βޱ಄ൃදͩͬͯR MarkdownͰͰ͖Δ
    26
    

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27. ࢀߟจݙ
    લా࿨׮ (2015). ʮRͰυΩϡϝϯτੜ੒Λ͠Α͏ʯ Kandai.R #1 Retrieved from
    http://kazutan.github.io/KandaiR1/rmd_intro.html#/
    લా࿨׮ (2016).ɹʮR MarkdownʹΑΔεϥΠυੜ੒ʯ SappoRo.R #6 Retrieved
    from https://kazutan.github.io/SappoRoR6/rmd_slide.html#/
    Mizumoto, A., Ikeda, M., & Takeuchi, O. (2016). A comparison of cognitive
    processing during cloze and multiple-choice reading tests using brain activation.
    ARELE (Annual Review of English Language Education in Japan), 27, 65–80.
    Murakami, A. (2016). Modeling systematicity and individuality in nonlinear
    second language development: The case of English grammatical morphemes.
    Language Learning. Advance Online Publication. doi:10.1111/lang.12166
    ਗ਼ਫ༟࢜ (2016).ɹʮSapporoR#6 ॳ৺ऀηογϣϯʯSappoRo.R #6 Retrieved
    from http://www.slideshare.net/simizu706/sapporor6
    27
    

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28. rmarkdownָ͍͠ʂ
    ݚڀͷ࠶ݱੑͷͨΊʹ
    contact info
    ాଜ ༞
    ໊ݹ԰େֶେֶӃੜ
    yutamura@nagoya-u.jp
    http://www.tamurayu.wordpress.com/
    28
    • R Markdown
    ίʔυͱ݁ՌΛυΩϡϝ
    ϯςʔγϣϯ
    • HTML
    • νʔτγʔτݟΕ͹୭Ͱ
    ΋Ͱ͖Δ
    • ࠔͬͨΒάάΕ͹
    

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