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The marinvaders (Marine Invaders) is tool to process data on marine invasive species from existing databases

Project description

The MarINvaders Toolkit

The MarINvaders Toolkit is a Python 3 module to assess the native and alien distribution of marine species.

It can be used to find the native and alien distribution of a given species or to get an overview of all alien and native species found in one marine ecoregion.

To do so, Marinivaders cross-references and harmonizes distribution maps from several databases to find all occurences of a given species and to gather information on its native and alien status per location recording. You can find the full documentation here.

Where to get it

The full source code and all requireded local data is available at the MarINvaders GitLab repostiory..

MarINvaders is registered at PyPI and at conda-forge for installation within a conda environment. To install use

pip install MariINvaders --upgrade

and when using conda:

conda update -c conda-forge MarINvaders

We recommend to install the package in a virtual environment or conda environment. See here for further information.

Getting started in five lines

Install the package as explained above and start your prefered Python interpreter

Import the package

import marinvaders

Get the species AphiaID you are interested in from the WoRMS - marine species database. Here we use * Amphibalanus amphitrite * (Darwin, 1854), aka the striped barnacle which has the AphiaID 421137.

Now we can get the species data from this barnacle with

species_data = marinvaders.Species(aphia_id=421137)

and list all occurences

species_data.all_occurrences

as well as the alien distribution of the barnacle with

species_data.reported_as_alien

These can also be easily plotted with

species_data.plot()

In addition, MarINvaders includes API functions for analysing all species within an ecoregion.

For a full overview of the capabilities see the example/tutorial notebook. This can also be run in the cloud through Binder:

Binder

Citations

Releases of MarINvaders are deposited at the Zenodo research repository and can be cited by their DOI: 10.5281/zenodo.4621393

DOI

Communication, issues, bugs and enhancements

Please use the issue tracker for documenting bugs, proposing enhancements and all other communication related to marinvaders. See the Contribution section of the docs for further information on code contributions.

License

This project is licensed under The GNU GPL v3

License: GPL v3

Project details


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