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EMODnet Biology Project Template

This repository contains a template for developing data products in the framework of EMODnet Biology.

Directory structure

{{cookiecutter.directory_name}}/
├── analysis
├── data/
│   ├── derived_data/
│   └── raw_data/
│   	└── data.csv
├── docs/
├── product/
└── scripts/
  • analysis - R Markdown or Jupyter Notebooks
  • data - Raw and derived data. The original raw data must not be modified.
  • docs - Rendered reports
  • product - Output product files
  • scripts - Reusable code

Getting started

To start a project using this template, you need to install cookiecutter first. Run the following statement in the command line to create a new project.

$ cookiecutter https://github.com/EMODnet/EMODnet-Biology-Project-Template

Alternatively, you can download this repository and modify the files yourself. The {{cookiecutter.directory_name}} folder is a github repository itself. You can substitute the tags {{cookiecutter.parameters}} in the README file under{{cookiecutter.directory_name}}/README.md by the correspondent information. The content of this tags is described below.

Parameters

This template will ask for the following input:

  • directory_name: The name of the new directory containing the project. This name must consist of the syntax "EMODnet-Biology-" followed by the name or acronym of your project without spaces nor special characters. An example would be "EMODnet-Biology-zooplankton-abundance"
  • project_name: The name of the project in plain text. This will be added to the README.md file. For example "Ecological niche model of zooplankton abundance"
  • project_description: A short description about the project. It will be added to the README.md file.
  • data_wfs_request: This is the query of the data that will be extracted from EMODnet-Biology. You can use the download toolbox to select the desired data. Once your query is ready, click on "Get webservice url" and copy the this link here. The data will be downloaded as .csv on ~/data/raw_data/. toolbox
  • citation: Include here the preferred citation for the product. This can be edited afterwards.

Contact

Please feel free to write some lines to [email protected] if you have any questions.