Last updated: 2019-04-09

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Knit directory: rrresearch/

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File Version Author Date Message
Rmd 3611edf Anna Krystalli 2019-04-09 update docs. add evolottery and collab_gh

Welcome to the evolutionary lottery of skull and beak morphology

#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.

Start!

💻 Clone a GitHub repo

Fork it

make your own copy of the repository on GitHub. Fork are linked and traceable

GitHub makes a copy into your account


🚦 Clone repo

copy repo link to create a new Rstudio project from the repository.

Create new project in Rstudio

Checkout from version control repository

Clone project from a git repository

Paste repo link copied from GitHub into Repository URL field. Click Create Project.

Rstudio project now contains all files from the GitHub repo.

🚦 Make a change to the repo

make a copy of params_tmpl.R

open params/params_tmpl.R

SAVE AS NEW .R script in params/ folder

Use species name of your choice to name new file.

Please DO NOT OVERWRITE params/params_tmpl.R.

🚦 Edit file

Edit file with parameters of your choice and save.

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: a character string e.g. "red", "#FFFFFF" (Check out list of colours in R)

NB: remember to save the changes to your file

🚦 Commit changes locally to git

In the git tab, select the new file you created and click Commit.

Please ONLY COMMIT YOUR NEW FILE

Write an informative commit message and click Commit

your new file has now been commited

Push changes to GitHub

on the git tab click ⇧ to push changes to GitHub

changes have now been updated in the GitHub repo


🚦 create pull request

In your repository, create new pull request to merge fork to master repo (ie the original repo you forked)

GitHub checks whether your requested merge creates any coflicts. If all is good, click on Create pull request

Write an informative message explaining your changes to the master repo administrators. Click on Create pull request

The repository owner will then review your PR and either merge it in or respond with some guidance if they spot a problem.

Check original repo to see your merged changes

We’ll merge all contributions and plot them together at the end!



R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
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 [4] emo_0.0.0.9000    crayon_1.3.4      assertthat_0.2.0 
 [7] digest_0.6.18     rprojroot_1.3-2   backports_1.1.3  
[10] git2r_0.24.0.9001 magrittr_1.5      evaluate_0.13    
[13] rlang_0.3.1       stringi_1.3.1     rstudioapi_0.9.0 
[16] fs_1.2.7          whisker_0.3-2     rmarkdown_1.12   
[19] tools_3.5.2       stringr_1.4.0     glue_1.3.1       
[22] purrr_0.3.2       xfun_0.5          yaml_2.2.0       
[25] compiler_3.5.2    htmltools_0.3.6   knitr_1.22