rmarkdown for reproducible...
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![Page 1: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/1.jpg)
Rmarkdown for Reproducible Research
Andrew Caines | Linguistics, Cambridge | apc38
27 November 2015
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 1 / 9
![Page 2: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/2.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)
plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 3: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/3.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by R
markdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 4: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/4.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)
R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 5: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/5.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunks
uses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 6: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/6.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion program
can produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 7: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/7.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documents
maintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 8: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/8.jpg)
What is R Markdown?
source file / output file paradigm (cp LaTeX, HTML, markdown)plain text file (.Rmd), rendered by Rmarkdown = plain-text authoring syntax, increasingly popular(e.g. GitHub)R Markdown = implementation of markdown, can take R codechunksuses knitr package (successor to Sweave) and ‘Pandoc’ text fileconversion programcan produce HTML, PDF and Word documentsmaintained by R Studio, now R Markdown v2
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 2 / 9
![Page 9: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/9.jpg)
What is R Markdown?
simple syntax: shallow learning curve
human-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 3 / 9
![Page 10: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/10.jpg)
What is R Markdown?
simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexity
transparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 3 / 9
![Page 11: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/11.jpg)
What is R Markdown?
simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwyg
embedded computation: share with collaborators, reviewers,colleagues, students, critics
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 3 / 9
![Page 12: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/12.jpg)
What is R Markdown?
simple syntax: shallow learning curvehuman-readable: emphasis on communication and clarity, ratherthan technique and complexitytransparent formatting: wysiwygembedded computation: share with collaborators, reviewers,colleagues, students, critics
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 3 / 9
![Page 13: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/13.jpg)
What is R Markdown?
. . . integrating source code, statistical output, and text in RMarkdown is a model of reproducibility.
Such transparency facilitates comprehension, defensibility, andfurther research or testing.
R Markdown helps to bring the vision for reproducibility instatistical analysis articulated by Gentleman & Temple Lang[2004] to reality.
Baumer & Udwin 2015, ‘R Markdown’, WIRES: ComputationalStatistics
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 4 / 9
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How to use R Markdown
installationinstall.packages('rmarkdown')
library(rmarkdown)
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 5 / 9
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How to use R Markdown
installationinstall.packages('rmarkdown')library(rmarkdown)
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 5 / 9
![Page 16: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/16.jpg)
How to use R Markdownsimple syntax, human-readable, transparent formatting
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 6 / 9
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How to use R Markdownembedded computation
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 7 / 9
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R Markdown and Reproducibility
User experience?
disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 19: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/19.jpg)
R Markdown and Reproducibility
User experience?disappointing :-/
Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 20: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/20.jpg)
R Markdown and Reproducibility
User experience?disappointing :-/Computational linguistics >(open) Linguistics
culture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 21: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/21.jpg)
R Markdown and Reproducibility
User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for example
Current project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 22: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/22.jpg)
R Markdown and Reproducibility
User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved on
Martijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 23: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/23.jpg)
R Markdown and Reproducibility
User experience?disappointing :-/Computational linguistics >(open) Linguisticsculture of Shared Tasks, for exampleCurrent project: proprietary data + 4p paper + no shared code +authors moved onMartijn Wieling’s statistics course: Rmd, HTML
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 8 / 9
![Page 24: Rmarkdown for Reproducible Researchbioinformatics-core-shared-training.github.io/reproducibility_worksho… · further research or testing. R Markdown helps to bring the vision for](https://reader035.vdocument.in/reader035/viewer/2022062317/5fcd047605a65b674c32e918/html5/thumbnails/24.jpg)
End
useful linksRStudio: R MarkdownUdwin & Baumer arXiv.org paper (= WIRES paper)Shiny & R Markdownmy GitHub ‘replication’ repo
contact meapc38my website[@cainesap](https://twitter.com/cainesap)
Andrew Caines | Linguistics, Cambridge | apc38Rmarkdown for Reproducible Research 27 November 2015 9 / 9