fauxneticien/kaytetye-medial-vowels: LabPhon submission version

About

This is the version of the analyses on 2019-02-14. Reproducibility of the analyses was verified in the rocker/verse Docker container running R 3.5.2.

Directory structure

This project follows a 'Cookiecutter Data Science' project template.

├── data
│   ├── external                             <- Metadata to be joined onto primary data
|   |   |── consonants.csv                   <- Categorized IPA consonant labels
|   |   |── headwords.csv                    <- Identities of Kaytetye words analyzed
|   |   |── headwords.csv                    <- Identities of Kaytetye words analyzed
|   |   |── raw-data_hashes.csv              <- Commit hashes of raw data sub-repos used
                                                in analyses
|   |   |── vowels.csv                       <- Categorized IPA vowel labels
│   ├── processed                            <- Intermediate data that has been transformed
|   |   |── micl_results.csv                 <- Results of Gaussian Mixture Model fits
|   |   |── vowels_med_analysis.csv          <- Primary data set of project
│   └── raw                                  <- Empty. Please contact for access to raw data
├── reports
│   ├── figures                              <- PDF figures used in manuscript
│   ├── manuscript                           
|   |   |── method.nb.html                   <- Method section, rendered to HTML
|   |   |── method.Rmd                       <- RMarkdown code used to generated
                                                method section
|   |   |── results+discussion.nb.html       <- Results and Discussion sections, rendered
                                                to HTML
|   |   |── results+discussion.Rmd           <- RMarkdown code used to generated Methods
                                                and Discussion sections
├── src                                      <- Source code for helper scripts
│   ├── visualization                        <- Helper scripts for figures
│   ├── data                                 <- Helper scripts for data analysis
|   |   ├── git                              <- Fetches/updates sub-repos in data/raw
                                                if you have access to them.
|   |   ├── make-micl_results.R              <- generates data/processed/micl_results.csv
|   |   ├── make-vowels_med_analysis.nb.html <- Outline of how vowels_med_analysis.csv
                                                was generated
|   |   ├── make-vowels_med_analysis.Rmd     <- generates vowels_med_analysis.csv
|   |   ├── mclust_helpers.R                 <- helper functions for make-micl_results.R
|   ├── setup.R                              <- Installs necessary R packages
├── .gitignore                               <- Files to be left untracked
├── .gitmodules                              <- Git URLs of linked private sub-repos
                                                in data/raw 
├── kayt_vowels.Rproj                        <- R Project file.
├── LICENSE                                  <- MIT license
├── README.md                                <- This README file

Recommended set up

1. Install Docker, and launch Docker

2. Clone/download this repository, e.g. to ~/Downloads/kaytetye-medial-vowels (n.b. file path)

3. Open up a Terminal instance and run:

   docker run -it --rm \
      -p 8787:8787 \
      -e PASSWORD=kayv \
      -v ~/Downloads/kaytetye-medial-vowels:/home/rstudio rocker/verse
   

4. Go to localhost:8787 in your browser, log in with username rstudio, password kayv

5. Run source("src/setup.R"). All analyses except those requiring access to data/raw are reproducible in this environment.