Research Methods: Open Science and Reproducible Research in Linguistics

# Research Methods: Open Science and Reproducible Research in Linguistics
## Createing RMarkdown website using blogdown
### Joseph V. Casillas, PhD
### Rutgers University</br>Spring 2019</br>Last update: 2019-05-02

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# **PART I**

### username.github.io

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# **PART I**

## Getting started

### Create username.github.io repo

- initiate w/ README
- make public

### Open github desktop

- clone username.github.io repo to desktop  
(if you plan on using/keeping site then pick a better place)

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# **PART I**

## Getting started

### Open RStudio

- create new project
- select username.github.io folder you just cloned

### Packages

- Update all packages
- Install "blogdown"

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# **PART I**

## Getting started

### In RStudio

- Create new .Rmd file
- Name it index.Rmd
- Delete everything except the yaml front matter
- Type a message in the text (anything)
- Save and knit

### Commit and push

- Select the "Git" pane, click "commit"
- In new window select all files and stage them (make the check mark appear)
- Type "initial commit" in the commit message box and click "commit"
- Push changes to github

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# **PART I**

## Getting started

### From github.com

- Go to username.github.io repo
- check to see it commits are there
- Click on the "settings" tab
- Scroll down to github pages section
- You should see "You site is published at..."
- Click on the link
- This is your webpage

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# **PART I**

## Getting started

### Details

- free webhosting from github.com
- this is the master of all masters
- any repo you make with the Github Pages setting set to "master" will be
	published from this website, i.e., username.github.io/REPONAME
- We have already seen this with our xaringan presentations

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class: title-slide-section-grey, middle

# **PART II**

### Blogdown

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# **PART II**

## Blogdown

### From RStudio

- type into the console: blogdown::install_hugo()
- This will probably take awhile
- After it finishes check for errors
- type this into the console: blogdown::new_site()
	- if you get an error, delete everything in your username.github.io folder (except the RStudio proj folder)

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# **PART II**

## Blogdown

### Lithium

- This is going to create an new website using the lithium theme
- This theme is ugly, but...
- Notice a few things...
- You should have a template blogpost open
- you get a preview in the Viewer pane
- Look at the username.github.io folder and check out what it did
- Go back to viewer pane and click the window/arrow icon to see site in web browser..  
--
have the basic idea? Ok...

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# **PART II**

## Blogdown

### Changing themes

- There are over 90 themes: https://themes.gohugo.io
- Common themes for academic webpages
	- https://github.com/kakawait/hugo-tranquilpeak-theme
	- https://github.com/kishaningithub/hugo-creative-portfolio-theme
	- https://github.com/devcows/hugo-universal-theme
	- https://github.com/gcushen/hugo-academic (this is the theme I use)

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# **PART II**

## Blogdown

### Changing themes

- Changing themes once you've started is difficult unless you burn the house down
- Let's burn the house down
	- delete everything in your username.github.io folder (except the RStudio proj folder)
	- type this into the console: blogdown::new_site(theme = "gcushen/hugo-academic", theme_example = TRUE)
- Explore the username.github.io folder, check the Viewer, expland to the web browser
- Now you know how to create a site and select a theme

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# **PART III**

### Your site

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# **PART III**

### Your site

- Create a new folder on your desktop (or near username.github.io) called "blogdown_source" 
- Create a new RStudio project for "blogdown_source"
- In the console: blogdown::new_site(theme = "gcushen/hugo-academic", theme_example = TRUE)
- Close template RMarkdown file
- Copy and paste: servr::daemon_stop(1)

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# **PART III**

### Your site

- Click the "Files" pane, open "config.toml"
	- baseurl: type in the url of your site ("https://username.github.io/")
	- publishDir: on the line below type the following...
		publishDir = "../username.github.io"
	- save and close "config.toml"
- In console: blogdown::build_site()
- Check username.github.io folder

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# **PART III**

### Your site

- Switch to username.github.io project
- Click Git pane, commit all files, push changes
- Check github.com to see if files were pushed
- Go to your website
- Yeah!!!

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# **PART IV**

### Customize your site

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# **PART IV**

### Customize your site

- Work from blogdown_source project
- blogdown::serve_site() (this will show live updates)
- Change config.toml file first
	- title = "Academic"
- config/_default/params.toml
	- color_theme = 
	- sharing_image = 
	- twitter = 
	- logo = 
	- email/phone/address etc.

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# **PART IV**

### Customize your site

- Content/author/admin/_index.md
	- bio
	- education
	- interests, etc. 
	- short bio (at bottom)
- This is enough to get you started, here is some more to help you customize
	- https://alison.rbind.io/post/up-and-running-with-blogdown/
	- https://bookdown.org/yihui/blogdown/

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# Summing up

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# Summing up

.big[
- Reproduction crisis
- Open science and reproducible research
- Registered reports, pre-registration
- Version control with git
- Literate programming and reproducible documents/projects
  - R 
  - RStudio projects
  - RMarkdown
]

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# Summing up

.big[
- Tidyverse
  - coding
  - plotting
  - manipulating data
- Dynamic documents for publication (papaja)
- HTML presentations
- Presenting stimuli using psychopy (offline/online)
- Website and blogs using blogdown
]

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# Summing up

.big[
- Research pipeline
  - Designing a project
  - IRB
  - Designing experiments
  - Running experiments
- Project oriented workflows
- OSF
  - Pre-registration
  - Finding and evaluating open materials
- Publishing
  - Selecting a journal
  - Manuscript preparation
  - Collaborating in github
  - Submitting a manuscript
]

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background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/teaching/gifs/rock_clap.gif)
background-size: contain

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class: title-slide-final, middle
background-image: url(https://github.com/jvcasillas/ru_xaringan/raw/master/img/logo/ru_shield.png), url(https://octodex.github.com/images/femalecodertocat.png)
background-size: 55px, 120px
background-position: 9% 15%, 89% 15%

# Getting help

## If you have problems
## ask for help on slack

### You can find some very basic tutorials related to 
### R, RStudio, RMarkdown, GitHub, and Slack [here][here]

[here]: http://www.jvcasillas.com/ru_teaching/ru_spanish_589/589_01_s2018/sources/tuts/index.html