trying this out
project
|- README.md # the top level description of content (this doc)
|- CONTRIBUTING.md # instructions for how to contribute to your project
|- LICENSE # the license for this project
|- CITATION # instructions on how to cite the work
|
|- study/
| |- header.sty # LaTeX header file to format pdf version of manuscript
| |- bibliography.bib # BibTeX formatted references
| |- csl/ # csl files to format references
| |- study.Rmd # executable Rmarkdown for this study, if applicable
| |- study.md # Markdown (GitHub) version of the *.Rmd file
| |- study.tex # TeX version of *.Rmd file
| |- study.pdf # PDF version of *.Rmd file
| |- study.html # html version of *.Rmd file
|
|- data # raw and primary data, are not changed once created
| |- references/ # reference files to be used in analysis
| |- raw/ # raw data, will not be altered
| |- processed/ # cleaned data, will not be altered once created;
| # will be committed to repo
|
|- docker # Files related to docker virtualisation
| |- Dockerfile # Dockerfile defining the development environment
| |- add_shiny.sh # These four files below are all configuration files
| |- disable_auth_rserver.conf # used in building an image from the Dockerfile
| |- pam-helper.sh # obtained from Rocker projects github page:
| |- userconf.sh # https://github.com/rocker-org/rocker-versioned/tree/master/rstudio
| # The Dockerfile has also heavily loaned code from the Rocker project:
| # https://www.rocker-project.org/
|
|- presentations # presentations about the project
| |- _output.yaml # shared configurations for all presentations
| |- style.css # css for modifying features in presentation
| |- presentation.Rmd # R revealjs presentation
| |- presentation.html # rendered html of presentation.Rmd
| |- images/ # images and other graphics for the presentation
|
|- code/ # any programmatic code
| |- test/ # tests for the code
|
|- results # all output from workflows and analyses
| |- tables/ # tables and other tabular data
| |- figures/ # graphs, likely designated for manuscript figures
| |- pictures/ # diagrams, images, and other non-graph graphics
|
|- exploratory/ # exploratory data analysis for study
| |- notebook/ # preliminary analyses
| |- scratch/ # temporary files that can be safely deleted or lost
|
|- Snakefile # executable Snakefile for this study, if applicable