#' ---
#' title: Create Final Project Webpage
#' subtitle: Data I/O. RMarkdown to create dynamic research outputs. Publishing to github/word/html/etc
#' week: 8
#' type: Task
#' reading:
#' - Chapters [11, 26-30 in R4DS](http://r4ds.had.co.nz)
#' - Browse website about [RMarkdown](https://rmarkdown.rstudio.com/index.html)
#' - Browse details about creating [RMarkdown Websites](https://rmarkdown.rstudio.com/rmarkdown_websites.htm)
#' presentation:
#' - PS_08_repro.html
#' tasks:
#' - Create repository for final project
#' - Explore various options for your project website
#' - Push changes back to GitHub
#' - Enable website on GitHub
#' - Complete DataCamp Course in [Reporting with R Markdown](https://www.datacamp.com/courses/reporting-with-r-markdown)
#' ---
#'
#'
#' `r presframe()`
#'
#' # Reading
#'
## ----reading,results='asis',echo=F---------------------------------------
md_bullet(rmarkdown::metadata$reading)
#'
#' # Tasks
#'
## ----reading,results='asis',echo=F---------------------------------------
md_bullet(rmarkdown::metadata$tasks)
#'
#' ## Overview
#' One convenient way to share research details is through a public website that includes all the information needed to reproduce the project. You will do this for your final project.
#'
#' 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/)
#'
#' ## R Markdown
#'
#' Cheatsheet:
#'
#' 
#'
#' ## Libraries
#'
#'
#' ## Create a copy of the project template.
#'
#' Steps:
#'
#' 1. Click on [this link](https://classroom.github.com/a/kCk9ysfI) to make a copy of the project template.
#' 2. Open your new repository in GitHub. It will look something like [https://github.com/AdamWilsonLabEDU/geo503-finalproject-adammwilson](https://github.com/AdamWilsonLabEDU/geo503-finalproject-adammwilson)
#' 3. Click the green button "Clone or Download" and copy the URL.
#'
#' ## Clone the project template to your computer
#' Now you will make a local copy on your computer by creating a new project and 'cloning' the repository you just forked.
#'
#' 1. **File -> New Project -> Version Control -> Git**
#' * URL: paste from above. It will be similar to `https://github.com/AdamWilsonLabEDU/geo503-finalproject-adammwilson` 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/AdamWilsonLabEDU/geo503-finalproject-adammwilson`
#' 3. Publish your website
#' * Click settings in the upper right, then scroll down to `GitHub Pages` section
#' * Change "Source" to `master branch /docs folder` and click Save
#' * Copy your new site's URL to your clipboard
#' * Go back to the 'Code' tab for your project respositor (similar to `https://github.com/AdamWilsonLabEDU/geo503-finalproject-adammwilson`) and find the line "No description, website, or topics provided" and click "Edit" on the right as shown in the following figure.
#' 
#' * Paste the URL in the "Website" box. This will make it easier for others to find your website.
#' 4. Go to your new project webpage (URL will be similar to `https://github.com/AdamWilsonLabEDU/geo503-finalproject-adammwilson`.
#' 5. Now you can `commit` and then `push` your updates from RStudio and your website will be updated. If you get tired of entering your username and password every time, check out the instructions [here](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.
#'