Reproducable & collaborative research with git

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# Reproducable & collaborative research with git
### Devin Judge-Lord

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![](Figs/git-fire.png)

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## Keep everything in one folder.
- Portability
- Replication
- Transparency

## Track version history.
- Restore code that breaks
- See what you or others did (e.g. why did our results change?!?)

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## Collaborating

#### With git-users 
- Line-by-line merging/diff (code and writing)

#### With non-users 
- Share document URLs (Word, LaTeX, whatever)
- Merge in their changes (LaTeX)
- Share HTML project updates (summary stats, draft figures, to-do lists)
- [Share data](https://github.com/jtleek/datasharing)

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## Repositories == Project folders

### + Subfolders
#### /data
#### /figs
#### /functions
#### /scratchpad

**Tip:** Use `source(setup.R)` in all scripts, where `setup.R` is a script that loads the packages and functions used in your project.

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## Finding things
`here()` makes valid file paths: [Ode to the here() package](https://github.com/jennybc/here_here)

```r
## This works no matter where a script is saved in the project folder
library(haven)
d <- read_dta(here("data/EX1.dta"))
glimpse(d)
```

```
## Observations: 20
## Variables: 2
## $ terms   <dbl> 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 6, 6,…
## $ Leg_Act <dbl> 2, 2, 9, -4, 7, 20, 9, 0, 11, 12, 0, 11, 16, 5, 9, 5, 6,…
```

**NEVER** use `setwd()` or user-specific file paths (e.g. `"C:\Users\path\that\only\I\have"`)!

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## Naming things!

**NEVER** name files untitled.R, data.csv, ProblemSet.Rmd, Rplot.png!

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## Basics

### To get started:
`git clone repositiory.url` in the terminal/consol.

(or, in RStudio, File -> New Project -> Version Control -> Git)

```{}
git config --global user.name "yourGitHubUserName"
git config --global user.email "yourEmail@email.com
```

(these do need to be done in the terminal/consol)

See a more details [here](http://r-pkgs.had.co.nz/git.html) and [this blog post](https://www.r-bloggers.com/rstudio-and-github/) for more detailed instructions for git setup in RStudio.

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## To do frequently
- `git commit` - confirm your changes
- `git pull` - merge in others' changes
- `git push` - update online repository

![](https://imgs.xkcd.com/comics/git_commit.png)

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## Avoid
- Useless commit messages
- Committing files > 100MB

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## Troubleshooting
- `git checkout` - restore a file from the online repo.
- `git reset` - read up on this before you do it!

![](https://imgs.xkcd.com/comics/git.png)

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## [GitHub](https://GitHub.com)
### Easily build a website
- Repository -> Settings -> GitHub Pages

### [GitHub pro is free for students](https://education.github.com/pack)
- unlimited collaborators on private repositories