The cookiecutter.sh file can help you to build a well-structured repository. You can use it by double-clicking the file, no command line arguments needed. Yue (Tina) Qian created the cookiecutter on November 18th, 2017.
The repository is named "project". There are 6 folders and 5 Markdown files in the root directory. The 5 files are "README", "LICENSE", "CITATION", "CONDUCT" and "CONTRIBUTION". The "README" file should contain sufficient information so that someone unfamiliar with your project could understand the overall aim of the project and be able to take your repository and reproduce your analysis on their machine. As their names indicated, corresponding information can be put into the other files.
The 6 folders are "bin", "data", "doc", "from_joe", "results", and "src". The "bin" folder is where you put external scripts or compiled programs; "data" is where you put raw data used in the project; "doc" is where you put text documents associated with the project. A manuscript.md file is created for your convenience; "from_joe" is where you put not used but important information for the project; "src" is where you put all code written for the project; and "results" folder is where you put all you analyzed information, including cleaned data sets, simulated data sets, intermediate results, and final results (such as figures and tables). The 4 sub-folders are created for your convenience.
The structure of the project folder is shown in the diagram below:
|-- CITATION.md
|-- README.md
|-- LICENSE.md
|-- CONDUCT.md
|-- CONTRIBUTION.md
|-- data
|-- doc
| -- manuscript.md
|-- results
| -- cleaned_data
| -- simulated_data
| -- intermediate_results
| -- final_results
|-- src
|-- from_joe
|-- bin