---
title: "Reproducible Research and R Markdown"
date: 2018-10-10
subtitle:
reading:
-
presentation:
- day_13_repro.html
tasks:
- Learn how to read R help files effectively
- Learn how to search for help
- Learn how to create a Minimum Working Example (MWE)
---
## Download
| [
R Script]( scripts/07_Reproducibile_nocomments.R ) | [
Commented R Script]( scripts/07_Reproducibile.R ) | [
Rmd Script]( scripts/07_Reproducibile.Rmd )|
|:--:|:-:|:-:|
## R Markdown
Cheatsheet:
[https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf)
## Overview
Today we will make a copy of a template for your final project, edit it, and 'push' it back up to your github account. You can check out the template code at [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) and the template website at [http://adamwilson.us/RDataScience_Project/](http://adamwilson.us/RDataScience_Project/)
## `Fork` the repository to create a linked copy in your GitHub account.
Steps:
1. Go to https://github.com/AdamWilsonLab/RDataScience_Project
2. Log into Github using your account (or create a new account)
3. Click `fork` near the upper right corner. This will create a copy in your GitHub Account. [See here for more details](https://help.github.com/articles/fork-a-repo/)
4. After it completes, click the green button "Clone or Download" and copy the URL.
## Clone the project template to your computer
1. **File -> New Project -> Version Control -> Git**
* URL: paste from above. It will be similar to `https://github.com/AdamWilsonLab/RDataScience_Project.git` but with your username.
* Project name: you can rename it if you want or keep the default: `RDataScience_Project`
* Project as subdirectory of `~/Documents/repos` or wherever you want to put it.
2. It should download the project to your computer then open it to the `index.Rmd` file.
## Play with the project template
1. Select the `Build` tab in the upper right corner of RStudio, then click `Build Website`
2. Check out the website settings in `_site.yml`. These adjust the appearance, title, etc.
3. Check out `_navbar.yml`. These settings define the menus, etc. If you only have one page you probably won't need to adjust this information.
## Push to GitHub and enable the website
1. Select the `Git` tab in the upper right and notice how it keeps track of any changes.
* To 'commit' the files (which is like saving them), check the files you want to commit (or all of them) and click `commit`.
* Type in a brief message about the changes you made. Maybe something like "First update to my project materials"
* Click `Commit`, then `close`.
* Click `Push` to push it back up to GitHub.
2. Now go to your repository website (similar to [https://github.com/AdamWilsonLab/RDataScience_Project](https://github.com/AdamWilsonLab/RDataScience_Project) in your account)
3. Click settings in the upper right, then scroll down to `GitHub Pages` section
* Source: `master branch /docs folder`
4. Go to your new project webpage (URL will be similar to [http://adamwilson.us/RDataScience_Project/]( http://adamwilson.us/RDataScience_Project/))
5. Now you can `commit` and then `push` your updates and your website will be updated. If you get tired of entering your username and password every time, check out the instructions [here](http://adamwilson.us/RDataScience/GitSSHNotes.html).
## Explore markdown functions
1. Use the Cheatsheet to add sections and some example narrative.
2. Try changing changing the species name to your favorite species and re-run the report.
3. Add more figures or different versions of a figure
4. Check out the `kable()` function for tables (e.g. `kable(head(d))`)
> Abandoning the habit of secrecy in favor of process transparency and peer review was the crucial step by which alchemy became chemistry.Raymond, E. S., 2004, The art of UNIX programming: Addison-Wesley.