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3-git.Rmd
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---
title: "Reproducable & collaborative research with git"
author: "Devin Judge-Lord"
date:
# output:
# html_document:
# toc: true
output:
xaringan::moon_reader:
lib_dir: libs
mathjax: "https://cdn.bootcss.com/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML"
css: templates/xaringan-themer.css
# css: [default, default, rladies-fonts]
nature:
highlightStyle: github
highlightLines: true
countIncrementalSlides: false
text_font_size: 2em
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
## Sets defaults for R chunks
knitr::opts_chunk$set(echo = TRUE, # echo = TRUE means that your code will show
warning=FALSE,
message=FALSE,
fig.retina = 2,
fig.align = "center",
dpi = 100,
# fig.path='Figs/', ## where to save figures
fig.height = 3,
fig.width = 3)
library(here)
source(here("setup.R"))
```
class: center
---
## 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?!?)
---
## 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)
---
## 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.
---
## Finding things
`here()` makes valid file paths: [Ode to the here() package](https://github.com/jennybc/here_here)
```{r here}
## This works no matter where a script is saved in the project folder
library(haven)
d <- read_dta(here("data/EX1.dta"))
glimpse(d)
```
**NEVER** use `setwd()` or user-specific file paths (e.g. `"C:\Users\path\that\only\I\have"`)!
---
## Naming things!
**NEVER** name files untitled.R, data.csv, ProblemSet.Rmd, Rplot.png!
<img height="600px" src="Figs/naming-animals.png">
---
## 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 "[email protected]
```
(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.
---
## To do frequently
- `git commit` - confirm your changes
- `git pull` - merge in others' changes
- `git push` - update online repository
---
## Avoid
- Useless commit messages
- Committing files > 100MB
---
## Troubleshooting
- `git checkout` - restore a file from the online repo.
- `git reset` - read up on this before you do it!
---
## [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