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

Project description

Marinvaders

The marinvaders [Marine Invaders] tool is an interactive tool that process data on marine invasive species from existing databases.

It enables the user to query, visualize and analyse information per marine ecoregion, and create maps that distinguish alien and natives distributions of a species.

Marine Invaders aims to facilitate the development of large-scale impact assessments of marine invasive species.

The Marine Invaders is developed and maintained by the Industrial Ecology Digital Lab and Francesca Research Group??? at the Norwegian University of Science and Technology in Trondheim, Norway.

Getting Started

These instructions will get you a copy of the project up and running on your local machine.

Installation from PyPI

pip install marinvaders --upgrade

Installation from conda-forge

coming soon

Usage

The marinvaders.ipynb jupyter notebook provides documentation and interactive tutorial on how to use this package.

The notebook is located either at: https://gitlab.com/dlab-indecol/marinvaders/-/blob/master/marinvaders.ipynb

or run in directly in mybinder:

Binder

Citations

TODO

Data sources

  • Marine Ecoregions of the World—MEOW

    Marine ecoregions are ecoregions (ecological regions) of the oceans and seas identified and defined based on biogeographic characteristics.

  • OBIS

    OBIS is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development

  • WoRMS

    World register of marine species.

  • GISD

    The Global Invasive Species Database is a free, online searchable source of information about alien and invasive species that negatively impact biodiversity.

  • Molnar

    The global database contains information on over 330 marine invasive species, including non-native distributions by marine ecoregion, invasion pathways, and ecological impact and other threat scores.

Data wrangling

The Marine Invaders tool currently integrates data on marine (invasive) species from four existing databases OBIS, WoRMS, GISD and a database by Molnar et al. After selecting an ecoregion, the OBIS API v3 is used to query all species for which there is occurrence data within that ecoregion in the OBIS database. Each species is then searched for in the latter three databases to potentially identify as alien. The WoRMS REST webservice is used to find the establishmentMeans –whether the species is flagged as alien or not-, whereas all species included in the GISD and Molnar databases as per definition alien. These databases provide geographical distributions on different scales. The Molnar distributions are on a marine ecoregion level. Most of the WoRMS distributions are either IHO Sea Areas, Exclusive Economic Zones (EEZ), or an intersect of these, and have a Marine Regions Geographic Identifier (MRGID) is easily matched to a marine ecoregion by the use of shapefiles. GISD does not provide such MRGID’s but instead gives only quantitative distributions, such as country names. Most of these could still be matched to existing shapefiles by comparing names, and subsequently be matched to marine ecoregions. All the distributions that could not automatically be matched were searched for manually and matched to one or more marine ecoregions.

Communication, issues, bugs and enhancements

Please use the issue tracker for documenting bugs, proposing enhancements and all other communication related to marinvaders.

Installation from source code

Alternatively the the software can be installed from source code. This is good in case of contributing or developing changes.

The project needs Python 3.7 and higher. For this project we recommend to use Anaconda Python Distribution.

Get copy of source code

The project is located at https://gitlab.com/dlab-indecol/marine-invaders

Either use Git to clone project or download the source code and unzip.

Install packages

Using terminal navigate to marine-invaders directory.

To install necessary packages use either conda the Anaconda package and environment management or Python virtual environment which is included in standard library since Python3.

Here are steps to create virtual environments for both options.

  • conda

    In terminal create new virtual environment inside the marine-invaders directory:

    `conda create env -f environment_dev.yml'

    This will create new environment marinvaders_dev with all packages installed for development.

    To use the envionment do conda activate marinvaders_development

  • Virtual Environment (Python3.7)

    In terminal create new virtual environment inside the marine-invaders directory:

    python3 -m venv env

    This will create new directory venv

    Activate the virtual environment:

    source env/bin/activate

    Install required packages:

    pip install -r requirements.txt

After installing and activating new environment (Note that the order is different in conda and Python) open IPython notebook

jupyter notebook MarineInvaders.ipynb

Jupyter is part of Anaconda distribution. If the Python3.7 is used then Jupyter must be installed in addition. For more information please refer to Jupyter project.

Authors

TODO

License

This project is licensed under The 3-Clause BSD License

Project details


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