07_Reproducibile.md

title	date	subtitle	reading	presentation	tasks
Reproducible Research and R Markdown	2018-10-10			day_13_repro.html	Learn how to read R help files effectively Learn how to search for help Learn how to create a Minimum Working Example (MWE)

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R Markdown

Cheatsheet:

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 and the template website at 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
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 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/)
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.

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.