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MarINvaders documentation

The MarINvaders Toolkit

The MarINvaders Toolkit is a Python 3 module to assess the native and alien (non-native) 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, MarINvaders cross-references and harmonizes distribution maps from several databases to find all occurrences 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 required local data is available at the MarINvaders GitLab repository..

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

pip install MarINvaders --upgrade

and when using conda:

conda install -c conda-forge MarINvaders

We recommend to install the package in a virtual environment or conda environment. See here for further information (including how to make the environment discoverable in your JupyterLab..

Getting started in five lines

Install the package as explained above and start your preferred 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 occurrences 

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 analyzing 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 and data terms of use

This project is licensed under The GNU GPL v3

License: GPL v3

This license only applies to the source code, for the licenses of the data processed by the modules see

Required data sources - terms of use:

  • WoRMS/marinespecies: http://marinespecies.org/about.php#terms
  • OBIS: https://obis.org/manual/policy/
  • NatCon: https://www.conservationgateway.org/ConservationPractices/Marine/Pages/marineinvasives.aspx see https://www.conservationgateway.org/Pages/Terms-of-Use.aspx

IUCN/optional data - terms of use

This data is not allowed to redistributed and most be downloaded manually. For more information see the documentation

  • ICUN GISD: http://www.iucngisd.org/gisd/legal.php
  • ICUN Red List: https://www.iucnredlist.org/terms/terms-of-use