#' ---
#' 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)
#' ---
#'
#'
#'
#' `r presframe()`
#'
#' ## Download
#'
#' `r output_table()`
#'
#'
#' ## 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.