Practical: GitHub & Rstudio for collaborative coding
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
.R script in params/ folder
Use species name of your choice to name new file.
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 5species.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.
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):
[1] workflowr_1.2.0 Rcpp_1.0.1 lubridate_1.7.4
[4] emo_0.0.0.9000 crayon_1.3.4 assertthat_0.2.0
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[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