class: center, middle, inverse, title-slide # Git: Hands-on ## <br>Practical Reproducibility ### John Little ### 2018-09-25 --- exclude: true --- class: middle, center Part of the ### Building Blocks for Reproducibility & ### [RFun](http://rfun.library.duke.edu) Learning Series ??? This is a presenter comment for the presenter mode use 'p' to toggle the presenter mode or '?' or 'h' to toggle the help / key-shortcut options --- class: middle, center ### Goal # Compose a Reproducible Document Use Git to manage version control Clone • Pull • Add • Commit • Push (Branch • Merge • Revert • Fork • Collaborate) --- class: middle, center ## Reproducible Research ### Open / Transparent ### Version Control ### Literate Code ### Collaborative --- class: middle ## Why RStudio? - **Reproducibility** is a Top Priority - Seamless IDE integration between R & Git - [Markdown](https://rmarkdown.rstudio.com/) - **Git for Version Control** - Git can be a pain to configure but works well in the background - Leapfrog beyond the barrier of a painful configuration - **RStudio orchestrates Git** - Alternative GUI Git Clients - [Sublime's Merge](https://www.sublimemerge.com/) - GitKracken (if you have the [GitHub Student](https://education.github.com/pack) Pack) - [SourceTree](https://www.sourcetreeapp.com/). (defaults with [BitBucket](https://bitbucket.org/)) --- class: middle # Part 2: Social Coding - GitHub (especially with Student Pack) - GitLab or Duke's instance of GitLab - Bitbucket.org or GitLab.com --- class: middle, center, duke-softblue # Reproducibility --- class: middle Karl Broman's *[initial steps toward reproducible research](http://kbroman.org/steps2rr/)* - Organize your data and code - [Everything with a script](http://kbroman.org/steps2rr/pages/scripts.html) - Automate the process - Turn scripts into reproducible reports - Turn repeated code into functions - Package functions for reuse - Use version control - License your software --- class: middle ## Broman: Everything with a script The most basic aspect of **reproducible research** is that **everything you do** (convert data files, clean data, analyze data) should be **accomplished via code.** *Pointing and clicking, and copy-paste, are not reproducible.* ??? Goal: Compose a Reproducible Document **in RStudio** --- class: middle, center Avoid ## Idiosyncratic Critical Steps so your processes **are not** reduced to ## Weird Bits of Undocumented Manual Magic ??? For Example... 1. Create Summary **Table in STATA** 2. **Copy** Table to MS **Excel** 3. **Format Table** for readability in Excel 4. Generate **Visualizations** in Excel 5. Integrate Excel Table into **Word > PDF** --- class: middle, center, duke-softblue # Version Control --- class: middle, center ## Version Control  ??? RStudio will manage the most commonly used Git commands --- class: middle, center  --- class: middle, center background-size: contain  --- class: center, middle, duke-softblue ## **Git** is a *Version Control System* --- class: bottom, right background-image: url(images/flickr_RupertsDogBoye_trail.jpg) .small-beige[ Image Credit: [Brandon Rasmussen](https://www.flickr.com/photos/137029081@N02/30943501632/in/photostream/) ] ??? Versioning can be used - as a kind of **breadcrumb system** that helps track the **research process/workflow** - Using version control, one can **easily "roll back"** to an earlier moment in the research workflow. - Leave a documented - **trail of where you've been** - how you got there - generated as you go --- ## Repositories .pull-left[ <figure><img src="images/repository_small.jpg" alt="image stack"><figcaption> Image Credit: <a href="https://www.flickr.com/photos/dbloete/274563369">Dennis Reimann</a></figcaption></figure><br> - Source Code Management - Track changes in any file set - Add • Commit • Branch • Merge • Revert ] .pull-right[ <figure><img src="images/file-extensions.png"><figcaption> Image Credit: <a href="https://openclipart.org/detail/192197/file-extension-icons">OpenClipart.org</a></figcaption></figure><br> ] ??? ### Source Code Mangement By this I simply mean **version control on a personal level**. Once can "branch" stages of research and merge successful operations. In this way it becomes easier to keep track of the process and the progress. ### Tracking changes in **any file set** **Git** can be used to **track any files**. --- class: duke-softblue, middle, center ## Markdown --- class: bottom background-image: url(images/rmarkdown.png) .small-txt[ Image Credit: [RStudio](http://rmarkdown.rstudio.com/) ] ??? R Markdown -- when combined with various R packages -- makes R a flexible report generation system. Thus R Notebooks become "literate code" where reports are an outcome of analysis. If analysis changes at "run-time" reports can change as integrated parts of the whole. Notably: **You Don't have to be a coder** to benefit from Version Control and R Markdown. The two method/features can be used to compose all of your reporting needs, including MS Word, PDF, LaTex, WebPages, WebSites, Slides, e-books, etc. I want to emphasize that *R* and *Git* are ideal for *reproducible research*. However, the added factor of **R Markdown** -- when combined with various R packages -- makes R a flexible report generation system, arguably more *open* and *reproducible* than other proprietary collaborations systems. --- class: middle .pull-left[ ``` # Heading ## Sub-heading ### Another deeper heading Text attributes *italic*, **bold**, `monospace`. A [link](http://google.com). Bullet list: - apples - oranges - pears Numbered list: 1. apples 2. oranges 3. pears ``` ] .pull-right[ ## Sub-heading ### Another deeper heading *italicized*, **bold**, `monospace` A [link](http://google.com) Bullet list: - applies - oranges - pears Numbered list: 1. apples 2. oranges 3. pears ] --- class: middle, center ## Hands-on [Excercise](../handson.html) --- ## Thank You For Attending .pull-left[ ### I am ... - **John Little** - https://johnlittle.info - https://github.com/libjohn #### Schedule Me - [http://v.gd/littleconsult](http://duke.libcal.com/appointment/2695) ### With... - Sophia Lafferty-Hess - Jen Darragh - [library.duke.edu/data/../staff/](https://library.duke.edu/data/about/staff/) ] .pull-right[ ### We are... - Data & Visualization Services - [library.duke.edu/**data**](http://library.duke.edu/data) - The /Edge, Bostock (1st Floor) #### Walk-in Hours - [Schedule](http://library.duke.edu/data/about/schedule) #### Our Workshops - [Rfun](http://rfun.library.duke.edu/) - [Current Workshops](http://library.duke.edu/data/news) - [Past Workshops](http://library.duke.edu/data/news/past-workshops) #### Contact Us - askData@Duke.edu ] --- class: center, middle ## Shareable Data, presentation, and handouts <span class="cc"> <!-- Key: a: SA, b: BY, c: CC Circle, d: ND, n: NC, m: Sampling, s: Share, r: Remix, C: CC Full Logo --> C bn </span> [CC BY-NC license](https://creativecommons.org/licenses/by-nc/4.0/)