R & Markdown for Research Students

# R & Markdown for Research Students
### Ben Marwick
### 04 April 2018

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# Motivation

![](images/Marwick et al Fig 2 reproducible research spectrum.1200x1200.jpeg)

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![](images/deadline.png)

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# How can R & Markdown help with common problems of dissertation writing?

.large[ Getting & staying organised] 
.large[ Citation & cross-referencing management] 
.large[ Formatting multi-part documents] 
.large[ Backing up files]

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# Why write in Markdown?

.large[ Simple text formatting system] 
.large[ 80% can be learned in 5 mins] 
.large[ Extensible via LaTeX] 
.large[ Plain text, cross-platform, flexible outputs]

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![](images/md-example.png)

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![](images/rmarkdownoutputformats.png)

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![](images/r-markdown-demo.png)

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# Getting & staying organised with Markdown & R

.large[ One chapter = one md file] 
.large[ Images by reference only] 
.large[ Figure and table citation and cross-referencing is abstracted]

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![](images/md-image-example.png)

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![](images/md-crossref-example.png)

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# Easy citations & bibliographies with Markdown & R

.large[ Uses Bibtex system] 
.large[ Get bib format entries from Google Scholar & Zotero et al. ] 
.large[ Very large variety of styles possible]

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![](images/md-bib-example.png)

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![](images/md-biblio-example.png)

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![](images/md-citr-demo.gif)

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# Multipart documents made easy

.large[ [Bookdown](https://bookdown.org/yihui/bookdown/) pkg for R] 
.large[ Write in many Rmd files & combine into one book] 
.large[ Apply complex styles & templates]

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![](images/huskydown-github.png)
https://github.com/benmarwick/huskydown
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![](images/huskydown-demo.gif)
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![](images/kieran-healy-workflow-wide.png)

Kieran Healy's "The Plain Person’s Guide to Plain Text Social Science" , http://plain-text.co

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# Backing up files & and sharing with others

.large[ Git is a version control and collaboration system ] 
.large[ R & Markdown work well with Git] 
.large[ GitHub and many others offer free private storage for Git repositories]

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![](images/draw-owl.jpg)

It can be hard to go from simple examples to the real thing we actually want.

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# R & Markdown are an easy way to make research more reproducible & transparent

![](images/Marwick et al Fig 2 reproducible research spectrum.1200x1200.jpeg)

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# To conclude

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# Colophon

Compiled into HTML5 using [RStudio](http://www.rstudio.com/ide/) & [knitr](http://yihui.name/knitr)

Source code hosting:
https://github.com/benmarwick/

ORCID: http://orcid.org/0000-0001-7879-4531

Licensing:

* Presentation: [CC-BY-3.0](http://creativecommons.org/licenses/by/3.0/us/)

* Source code: [MIT](http://opensource.org/licenses/MIT) ]