/collaborative_github_exercise

Primary LanguageRMIT LicenseMIT

collaborative github exercise:

Welcome to the evolutionary lottery of skull and beak morphology


Beak and skull shapes in birds of prey (“raptors”) are strongly coupled and largely controlled by size.

gif provided by the awesome Jen Bright @MorphobeakGeek!

In this exercise we will use a github repo to collaboratively collate and simulate evolutionary trajectories for each participants' species body size using a simple brownian motion evolutionary model. This assumes evolutionary steps to progress comletely at random. You could say, it's a bit of lottery!

our mission

  • Each participant will create and contribute a file specifying the parameters required to simulate and plot their species evolutionary trajectory.
  • We'll collect all participants' files in the master repo.
  • Once all trajectories are simulated they'll be plotted together.
  • Participants will then get to see the skull and beak shape corresponding to their species relative body size!

Next Session: Join Remotely!

MozFest 2016: Saturday, 29 Oct 1:00pm-3:00pm

Collaboration through Github and Rstudio

We'll be accepting pull requests by remote participants between 2.00 - 3.00 pm, so anyone can get involved! Follow #EvoLottery on the day for live updates on twitter.


GO!

link to full session handout

github: fork

  • fork the repo into your own account
  • copy repo url link local files to github repo

rstudio: clone locally

  • create new project
  • checkout from version control/git
  • paste github repo link

rstudio: create parameter .R script

A template is provided in the repo, in folder /params named params_tmpl.R. Open the params_tmpl.R and save as to create a duplicate template. Name the template using the name of your species.


rstudio: edit your params .R script

The parameters each participants need to supply are:

  • sig2: A numeric value greater than 0 but smaller than 5

  • species.name: a character string e.g. "anas_krystallinus". Try to create a species name out of your name!

  • color: e.g. "red", "#FFFFFF" (tip: pick a color using Rstudio's Color picker:)


rstudio: save and commit the changes

  • Use the git tab, tick the box next to your new script and commit.

  • Supply a descriptive message of the commit.


rstudio: push to github

  • push your changes to github

github: create pull request

  • create a pull request to merge your changes to the master repo

github: check to see my response to your request

  • most likely it'll be a thumbs up! But I might also request a correction if I spot an error.

Once all parameters are collated, look out for the results!

Links to previous evolution lottery sessions: