What is Version control? 🤔

The management of changes to documents, computer programs, large web sites, and other collections of information.

Examples:

• Numbering of book editions
• Wikipedia’s Page history

What is git? 🤔

Open source (free to use) Version control software. Usually accessed via the command line, or a client program.

Why use it in research?

Exhibit A

---

What is GitHub 🤔

A website that allows you to store your Git repositories online and makes it easy to collaborate with others. They also provide other services like issue (bug) tracking and wikis. Similar services are GitLab and BitBucket.

Git, Github & Rstudio

How does Git work?

When a local directory becomes initialised with git, a hidden .git folder is added to it.

it’s now called a repository

• New copies of files you tell git to track will be added to that .git folder.

• After adding, git will track any modifications to those files

Configure git

First, git needs to know who you are so your commits can be attributed to you. usethis to the rescue again!

Check your configuration

usethis::use_git_config()

Set your configuration

Use your github username and and the email you used to sign-up on GitHub

usethis::use_git_config(
    user.name = "Jane",
    user.email = "jane@example.org")

🚦 Set up GITHUB PAT

To authenticate with GitHub, you’ll also need a Personal Authorisation Token (PAT).

usethis::browse_github_pat()

will open up the GitHub panel to generate your PAT.

Copy it and paste it into your .Renviron file as system variable GITHUB_PAT.

usethis::edit_r_environ()

Use edit_r_environ() to open and edit your .Renviron file

Turn our project into a repository

If you didn’t initialise git at the beginning of your project, you can do so now with:

usethis::use_git()

This however commits everything in one go. So not ideal! I recommend using git from the start of every project.

Add files

To commit changes in a file just select it in the git pane. When changes to a file are commited for the first time, the whole file is indicated as Added (green A).

Commit changes

Click on commit and write an appropriate commit message:

Edit README

Adapt the template, adding a short description about your project.

Add and commit your new README

Create repository

Now that we have set up a GITHUP_PAT, we can use function usethis::use_github() to create a GitHub repository for our project:

usethis::use_github(protocol = "https")

push files

Click on the ⬆️ button on the Git tab to push our changes up to our newly minted repository

Let’s go have a look at the history 🕒

Making a change to our gapminder-analysis.Rmd

• In the last plot of your .index.Rmd, see if you can add a smooth for each continent to generate the plot below (should be just one extra ggplot2 function added to the plot). Look for the appropriate geom_* function.

• See also if you can include an interactive plotly version

Past versions of unnamed-chunk-9-1.png

Commit your changes

On the commit window:

• Have a look at the differences

• Have a look at the history

Go to repo Settings

Enable gh-pages

Review setup

Ensure the Enforce HTTPS option is selected.

Click on the link displayed and go check out your work!

Copy the link. In the main repo page, edit the page details at the top and paste copied the url in the website field.

Create LICENSE

Let’s create also create a LICENSE in our repository.

Add link to analysis index.html to README

Let’s edit the README.md on GitHub to add

Commit the changes directly into the master again.

🚦 Pull changes locally

Finally, let’s pull the changes back down to our local repository by clicking the ⬇️ button on the Git tab.

🚦 Deleting files

• Create a new file, any type of file.

• Commit it.

• Delete it

• Commit the deletion

• Look back through the history

gitignore regex

You can use regex in .gitignore files to ignore files according to a pattern.

• *.html will ignore any file ending in .html

• prefix “!” which negates the pattern

  data/*
  !data/commit-this.csv

Further Resources

• Git-it
• Happy with Git
• Oh Shit Git

Never forget

Session information

sessionInfo()

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     

other attached packages:
[1] ggplot2_3.1.1   dplyr_0.8.0.1   gapminder_0.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        compiler_3.5.2    pillar_1.3.1     
 [4] git2r_0.25.2.9000 plyr_1.8.4        workflowr_1.2.0  
 [7] tools_3.5.2       digest_0.6.18     lubridate_1.7.4  
[10] evaluate_0.13     tibble_2.1.1      gtable_0.3.0     
[13] pkgconfig_2.0.2   rlang_0.3.4       rstudioapi_0.10  
[16] yaml_2.2.0        xfun_0.5          emo_0.0.0.9000   
[19] withr_2.1.2       stringr_1.4.0     knitr_1.22       
[22] fs_1.2.7          rprojroot_1.3-2   grid_3.5.2       
[25] tidyselect_0.2.5  glue_1.3.1        R6_2.4.0         
[28] rmarkdown_1.12    purrr_0.3.2       magrittr_1.5     
[31] whisker_0.3-2     backports_1.1.3   scales_1.0.0     
[34] htmltools_0.3.6   assertthat_0.2.0  colorspace_1.4-0 
[37] labeling_0.3      stringi_1.3.1     lazyeval_0.2.2   
[40] munsell_0.5.0     crayon_1.3.4