project
|- README          # the top level description of content (this doc)
|- CONTRIBUTING    # instructions for how to contribute to your project
|- LICENSE         # the license for this project
|
|- submission/
| |- 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
| |- header.tex   # LaTeX header file to format pdf version of manuscript
| |- references.bib # BibTeX formatted references
| |- XXXX.csl     # csl file to format references for journal XXX
|
|- 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
| |- mothur/      # mothur processed data
|  - process/     # cleaned data, will not be altered once created;
|                 # will be committed to repo
|
|- code/          # any programmatic code
|
|- results        # all output from workflows and analyses
| |- tables/      # text version of tables to be rendered with kable in R
| |- 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
|
 - Makefile       # executable Makefile for this study, if applicable