Research Methods: Open Science and Reproducible Research in Linguistics

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# Research Methods: Open Science and Reproducible Research in Linguistics
## Reproducible projects<br>Version control II: RStudio
### Joseph V. Casillas, PhD
### Rutgers University</br>Spring 2019</br>Last update: 2019-02-21

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# More about projects

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# Workflows and projects

### What does your workflow currently look like?

### What do you organize for?

### How do you do it?

### Where do your files live?

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# RStudio projects

### If your projects include R scripts, RMarkdown documents, HTML slides, etc., you should be using RStudio projects

- What are they?

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`.rproj` files create an independent RStudio environment that limits the scope of your R session to the project in question.
]

- Why use them?

- They simplify organizing projects
  - They integrate well with github
  - They promote a project-oriented workflow

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# What's in a project anyway?

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# Directory structure

### Student

.big[
- class notes
- articles
- misc. documents
- final project
- homework
]

background-image: url(./assets/img/student_project.png)
background-size: 700px
background-position: 95% 50%

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background-image: url(./assets/img/student_project.png)
background-size: contain

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# Directory structure

### Researcher

.big[
- data
- scripts
- manuscript
- slides
- READMEs
]

background-image: url(./assets/img/researcher_project.png)
background-size: 700px
background-position: 95% 50%

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background-color: black
background-image: url(./assets/img/researcher_project.png)
background-size: contain

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# Directory structure

### A note on READMEs

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- Every folder/directory should have a README.md file that explains...
  - the purpose of the folder
  - the contents of the folder
  - any keys/glossaries necessary to understand the contents of the folder
  - timestamps
  - etc.

]

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# Say my name

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# Naming conventions

### Why?

- You probably don't spend much time thinking about how you name files and documents

- You should

- The idea is to follow a few simple guidelines that will make facilitate 
organizing your projects and make the file structure easily searchable

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# Naming conventions

### How?

.pull-left[

- Use descriptive names 
  - .red[Bad]: `Experiment`
  - .green[Good]: `qualifying_paper_1`

- no capitals, no spaces (use `_` or `-`)
  - .red[Bad]: `Experiment for syntax class`
  - .green[Good]: `semantic_predictability_exp_1`

- no non-standard characters
  - .red[Bad]: `Analysis of ð for ICPhS 2019`
  - .green[Good]: `spirantization_icphs_2019`

]

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- Numbers: use 2 places minimum, year-month-day
  - .red[Bad]: `Analysis 1`
  - .blue[Better]: `01_analysis`
  - .green[Best]: `2019-02-20_data_download`

]

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background-size: 400px
background-position: 90% 90%

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# Github integration

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# Tips and tricks

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# Tips and tricks

### Nested projects

- You can have RStudio projects inside of larger projects
- Only the larger project is a repo
- Ex.  
  - Project: `dissertation` (← repo)
  - Nested project: `production_semantic_processing_las`
  - Nested project: `prod_perc_bilabials_jphon`

### Alfred

- Productivity app 
- Only on Mac (I think), free
- Works like Spotlight search, but customizable
- Set to search for `.rproj` files
- Allows you to quickly open and close RStudio projects

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# Getting help

## If you have problems using RStudio projects 
## ask for help in the slack channel

### 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