Metadata-Version: 2.1
Name: marinvaders
Version: 0.0.7
Summary: The marinvaders (Marine Invaders) is tool to process data on marine invasive species from existing databases
Home-page: https://gitlab.com/dlab-indecol/marinvaders
Author: Radek Lonka
Author-email: radek.lonka@ntnu.no
License: BSD-3
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](https://academic.oup.com/bioscience/article/57/7/573/238419),
        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](https://iedl.no) 
        and *Francesca Research Group???* at the 
        [Norwegian University of Science and Technology](https://www.ntnu.edu) 
        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`
        
        
        ## 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 ar mybinder:
        TODO
        
        ## Citations
        TODO
        
        ## Data sources
        * [Marine Ecoregions of the World—MEOW](https://en.wikipedia.org/wiki/Marine_ecoregions)
        
            Marine ecoregions are ecoregions (ecological regions) of the oceans and seas identified
            and defined based on biogeographic characteristics.
        
        * [OBIS](https://obis.org/)
        
            OBIS is a global open-access data and information clearing-house on marine biodiversity
            for science, conservation and sustainable development
        
        * [WoRMS](http://www.marinespecies.org/index.php)
        
            World register of marine species.
        
        * [GISD](http://www.iucngisd.org/gisd/)
        
            The Global Invasive Species Database is a free, online searchable source of
            information about alien and invasive species that negatively impact biodiversity.
        
        * [Molnar](https://www.conservationgateway.org/ConservationPractices/Marine/Pages/marineinvasives.aspx)
        
            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](https://api.obis.org/) 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](http://www.marinespecies.org/rest/)
        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](https://www.anaconda.com/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](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
        the Anaconda package and environment management or 
        Python [virtual environment](https://docs.python.org/3/library/venv.html) 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 --name venv`
        
            This will create new directory **venv** 
            
            Install required packages:
        
            `conda install -f -y -q -n venv --file requirements.txt`
        
           Activate the virtual environment:
        
            `conda activate venv`
        
        - 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](https://jupyter.readthedocs.io/en/latest/install.html).
        
        
        ## Authors
        TODO
        
        ## License
        This project is licensed under The [3-Clause BSD License](LICENSE.md)
        
        
        
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Utilities
Requires-Python: >=3.7.0
Description-Content-Type: text/markdown
