class: top, left, inverse ## ACCE DTP ### _Reproducible Research Data and Project Management in R_ *** .bottom[ # Collaborative `Github` in `Rstudio` <br> **<svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M400 64h-48V12c0-6.6-5.4-12-12-12h-40c-6.6 0-12 5.4-12 12v52H160V12c0-6.6-5.4-12-12-12h-40c-6.6 0-12 5.4-12 12v52H48C21.5 64 0 85.5 0 112v352c0 26.5 21.5 48 48 48h352c26.5 0 48-21.5 48-48V112c0-26.5-21.5-48-48-48zm-6 400H54c-3.3 0-6-2.7-6-6V160h352v298c0 3.3-2.7 6-6 6z"></path> </svg> April-May 2021** <br> **<svg viewBox="0 0 288 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M112 316.94v156.69l22.02 33.02c4.75 7.12 15.22 7.12 19.97 0L176 473.63V316.94c-10.39 1.92-21.06 3.06-32 3.06s-21.61-1.14-32-3.06zM144 0C64.47 0 0 64.47 0 144s64.47 144 144 144 144-64.47 144-144S223.53 0 144 0zm0 76c-37.5 0-68 30.5-68 68 0 6.62-5.38 12-12 12s-12-5.38-12-12c0-50.73 41.28-92 92-92 6.62 0 12 5.38 12 12s-5.38 12-12 12z"></path> </svg> Online** ] --- # Session Roadmap <br> ### 1 Introductions #### - **get to know github** - github as a computational research tool --- # Session Roadmap <br> ### 2 Get stuck in #### - [Collaborative github through rstudio](https://nhm-stars.github.io/materials/day04/evolottery.html) #EvoLottery (40 mins) - In this exercise, each participant will fork a github repo, and contribute a file required to simulate the **evolutionary trajectory of an imaginary species' body size**. - We'll use github to collate all species files and plot them all up together at the end! We'll also **discover the skull and beak shapes** associated with each simulated species size. --- class: top, right, inverse # introductions: **get to know github** *** ## **GitHub features** --- #### Back up and sync through the cloud <div class="figure"> <img src="assets/remotes.png" alt="Image: Jessica Lord, 2013 BSD" width="90%" /> <p class="caption">Image: Jessica Lord, 2013 BSD</p> </div> --- #### Fork and contribute to other's work <div class="figure"> <img src="assets/clone.png" alt="Image: Jessica Lord, 2013 BSD" width="90%" /> <p class="caption">Image: Jessica Lord, 2013 BSD</p> </div> --- ## **GitHub for science** *** > - ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. > - supports peer review, commenting, and discussion. > - Diverse range of efforts, from individual to large bioinformatics projects, laboratory repositories, as well as global collaborations have found a home on GitHub <br> --- ### remote repositories centralising information e.g. [**weecology** / ***"Nine simple ways to make it easier to (re)use your data" paper***](http://ojs.library.queensu.ca/index.php/IEE/article/view/4608/0) | [Repo](https://github.com/weecology/data-sharing-paper) <img src="assets/repo-1.png" width="80%" /> --- ### commits traceability #### [Repo](https://github.com/ropensci/rfishbase/commits/master) <img src="assets/commits-1.png" width="90%" /> <br> --- ### issues project management #### [Repo](https://github.com/weecology/data-sharing-paper/issues) <img src="assets/issues-1.png" width="90%" /> <br> --- ### graphs #### project & team tracking: Tracking contributors [Repo](https://github.com/weecology/data-sharing-paper/graphs/contributors) <img src="assets/track-1.png" width="80%" /> --- tracking commits #### [Repo](https://github.com/weecology/data-sharing-paper/network) <img src="assets/track-2.png" width="90%" /> <br> --- class: center, middle, invert ## **entire process of project evolution reproducible** *** <br> --- class: top, right, inverse ## **Practical: Github & Rstudio for collaborative coding** *** --- ### **#EvoLottery** **Beak and skull shapes in birds of prey (“raptors”) are strongly coupled and largely controlled by size.** - In this exercise, each participant will **fork a github repo**, and **contribute a file** required to simulate the *evolutionary trajectory of an imaginary species' body size*. - We'll use **github** to **collate all species files** and **plot** them all up together at the end! We'll also **discover the skull and beak shapes** associated with each simulated species size. ### [**Enter Practical**](evolottery.html) ### See [**Collaborative plot**](https://rse.shef.ac.uk/collaborative_github_exercise/plot_trait_evolution.html) --- ## Get back [home](https://annakrystalli.me/rrresearchACCE20/)