Organizing and version control

# Organizing and version control
## Advanced Data Science
### Jeff Leek
### 2017-08-24

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Motivation

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# An exciting result

http://www.nature.com/nm/journal/v12/n11/full/nm1491.html

![](../imgs/potti.png)

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# Baggerly

https://projecteuclid.org/euclid.aoas/1267453942

![](../imgs/baggerly.png)

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# Timeline

http://www.nature.com/news/2011/110111/full/469139a/box/1.html

![](../imgs/timeline-potti.png)

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# Potti Fallout

http://dig.abclocal.go.com/wtvd/docs/Duke_lawsuit_090811.pdf

![](../imgs/potti-lawsuit.png)

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# Worth a watch!

https://goo.gl/T2nWbC

![](../imgs/baggerly-talk.png)

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# Not just the boogeyman

"Your closest collaborator is you six months ago, but you don’t reply to emails."

-Karl Broman

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![](../imgs/broman.png)
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http://kbroman.org/Tools4RR/assets/lectures/06_org_eda.pdf

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Organizing Projects

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"Your closest collaborator is you six months ago, but you don’t reply to emails."

-Jenny Bryan

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![](../imgs/bryan.png)
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http://kbroman.org/Tools4RR/assets/lectures/06_org_eda.pdf

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# Keys to success

*_Step 1_ slow down and document. 
*_Step 2_ have sympathy for your future self. 
*_Step 3_ have a system.

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# Not a good plan

http://www.slideshare.net/jenniferbryan5811/cm002-deep-thoughts

![](../imgs/ugly-files.png)

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# One strategy

* data
    - raw_data
    - processed_data
* figures
    - exploratory_figures
    - final_figures
* code
    - raw_code
    - final_code
    - rmarkdown
* text
    - README
    - writeup
]

]

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# One strategy

* data
    - raw_data
    - processed_data
* figures
    - exploratory_figures
    - final_figures
* code
    - raw_code
    - final_code
    - rmarkdown
* text
    - README
    - writeup
]

.pull-right[
* code/
    * final_code/
        - 0-preprocess.R
        - 1-explore.R
        - 2-model.R
        - 3-final-plots.R

]

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# Just...no

https://xkcd.com/1459/

![](../imgs/xkcd-filenames.png)

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# Version control

* Automatically tracks versions of documents
* Keeps a log of the entire history
* Let’s you “undo” your work
* Let’s you view what you changed

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# Unfortunate truth

https://twitter.com/mtrc/status/617075570761965568

![](../imgs/xkcd-filenames.png)

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# Version control options

* __Github__ - where the cool nerds are
* __Bitbucket__ - where the real nerds are
* __svn__ - where the old nerds are
* __Files on your desktop__ - where the frustrated nerds are

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# Github

https://github.com/

![](../imgs/github.png)

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# Why this is cool

![](../imgs/hammer-typo.png)

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# Git/Github workflow

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# Installing Git/Github

http://happygitwithr.com/install-git.html

![](../imgs/installing-git-github.png)

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# Let's do an example

![](../imgs/newproject1.png)

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Organizing Files

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# Three* principles of naming things

* machine readable
* human readable
* plays well with default ordering
* easy to type (added by me)
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https://goo.gl/6cv4wV