marinvaders


Namemarinvaders JSON
Version 0.0.8 PyPI version JSON
download
home_pagehttps://gitlab.com/dlab-indecol/marinvaders
SummaryThe marinvaders (Marine Invaders) is tool to process data on marine invasive species from existing databases
upload_time2021-02-09 18:20:57
maintainer
docs_urlNone
authorRadek Lonka
requires_python>=3.7.0
licenseGNU GPLv3
keywords
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # 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`


### 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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gl/dlab-indecol%2Fmarinvaders/master?filepath=marinvaders.ipynb)

## 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 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](https://jupyter.readthedocs.io/en/latest/install.html).


## Authors
TODO

## License
This project is licensed under The [3-Clause BSD License](LICENSE.md)
            

Raw data

            {
    "_id": null,
    "home_page": "https://gitlab.com/dlab-indecol/marinvaders",
    "name": "marinvaders",
    "maintainer": "",
    "docs_url": null,
    "requires_python": ">=3.7.0",
    "maintainer_email": "",
    "keywords": "",
    "author": "Radek Lonka",
    "author_email": "radek.lonka@ntnu.no",
    "download_url": "https://files.pythonhosted.org/packages/fd/53/7203167c83b3e8fcd7799754d95907b6cee8252ffefc6b1683ef7c0cb346/marinvaders-0.0.8.tar.gz",
    "platform": "",
    "description": "# Marinvaders\n\nThe marinvaders [Marine Invaders] tool is an interactive\ntool that process data on marine invasive species from \nexisting databases. \n\nIt enables the user to query, visualize and analyse information per \n[marine ecoregion](https://academic.oup.com/bioscience/article/57/7/573/238419),\nand create maps that distinguish alien and natives distributions \nof a species. \n\nMarine Invaders aims to facilitate the development \nof large-scale impact assessments of marine invasive species. \n\nThe Marine Invaders is developed and maintained by the \n[Industrial Ecology Digital Lab](https://iedl.no) \nand *Francesca Research Group???* at the \n[Norwegian University of Science and Technology](https://www.ntnu.edu) \nin Trondheim, Norway. \n\n\n## Getting Started\n\nThese instructions will get you a copy of the project up and running on\nyour local machine.\n\n### Installation from PyPI\n\n`pip install marinvaders --upgrade`\n\n\n### Installation from conda-forge\n\ncoming soon\n\n## Usage\n\nThe marinvaders.ipynb jupyter notebook provides documentation and interactive tutorial on how to use this package.\n\nThe notebook is located either at:\nhttps://gitlab.com/dlab-indecol/marinvaders/-/blob/master/marinvaders.ipynb\n\nor run in directly in mybinder:\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gl/dlab-indecol%2Fmarinvaders/master?filepath=marinvaders.ipynb)\n\n## Citations\nTODO\n\n## Data sources\n* [Marine Ecoregions of the World\u2014MEOW](https://en.wikipedia.org/wiki/Marine_ecoregions)\n\n    Marine ecoregions are ecoregions (ecological regions) of the oceans and seas identified\n    and defined based on biogeographic characteristics.\n\n* [OBIS](https://obis.org/)\n\n    OBIS is a global open-access data and information clearing-house on marine biodiversity\n    for science, conservation and sustainable development\n\n* [WoRMS](http://www.marinespecies.org/index.php)\n\n    World register of marine species.\n\n* [GISD](http://www.iucngisd.org/gisd/)\n\n    The Global Invasive Species Database is a free, online searchable source of\n    information about alien and invasive species that negatively impact biodiversity.\n\n* [Molnar](https://www.conservationgateway.org/ConservationPractices/Marine/Pages/marineinvasives.aspx)\n\n    The global database contains information on over 330 marine invasive species,\n    including non-native distributions by marine ecoregion, invasion pathways,\n     and ecological impact and other threat scores.\n     \n## Data wrangling\nThe Marine Invaders tool currently integrates data on marine \n(invasive) species from four existing databases OBIS, WoRMS, GISD \nand a database by Molnar et al. After selecting an ecoregion,\nthe [OBIS API v3](https://api.obis.org/) is used to query all \nspecies for which there is occurrence data within that ecoregion \nin the OBIS database. Each species is then searched for in the \nlatter three databases to potentially identify as alien. \nThe [WoRMS REST webservice](http://www.marinespecies.org/rest/)\nis used to find the establishmentMeans \u2013whether the species is \nflagged as alien or not-, whereas all species included in \nthe GISD and Molnar databases as per definition alien. \nThese databases provide geographical distributions on different \nscales. The Molnar distributions are on a marine ecoregion level. \nMost of the WoRMS distributions are either IHO Sea Areas, \nExclusive Economic Zones (EEZ), or an intersect of these, \nand have a Marine Regions Geographic Identifier (MRGID) is easily \nmatched to a marine ecoregion by the use of shapefiles. \nGISD does not provide such MRGID\u2019s but instead gives only \nquantitative distributions, such as country names. Most of these \ncould still be matched to existing shapefiles by comparing names, \nand subsequently be matched to marine ecoregions. \nAll the distributions that could not automatically be matched \nwere searched for manually and matched to one or more marine \necoregions. \n\n\n## Communication, issues, bugs and enhancements\n\nPlease use the issue tracker for documenting bugs, proposing enhancements and all other communication related to marinvaders.\n\n## Installation from source code\n\nAlternatively the the software can be installed from source code.\nThis is good in case of contributing or developing changes.\n\nThe project needs Python 3.7 and higher. For this project\nwe recommend to use \n[Anaconda Python Distribution](https://www.anaconda.com/distribution/).\n\n#### Get copy of source code \n\nThe project is located at https://gitlab.com/dlab-indecol/marine-invaders\n\nEither use Git to clone project or download the source code and unzip.\n\n\n#### Install packages\n\nUsing terminal navigate to marine-invaders directory. \n\nTo install necessary packages use either [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)\nthe Anaconda package and environment management or \nPython [virtual environment](https://docs.python.org/3/library/venv.html) which is\nincluded in standard library since Python3.\n \n\nHere are steps to create virtual environments for both options.\n\n- conda\n\n    In terminal create new virtual environment inside the marine-invaders directory:\n\n    `conda create env -f environment_dev.yml'\n\n    This will create new environment marinvaders_dev with all packages installed for development. \n    \n    To use the envionment do\n    `conda activate marinvaders_development`\n\n\n- Virtual Environment (Python3.7)\n\n    In terminal create new virtual environment inside the marine-invaders directory:\n\n    `python3 -m venv env`\n\n    This will create new directory **venv** \n\n    Activate the virtual environment:\n\n    `source env/bin/activate`\n\n    Install required packages:\n\n    `pip install -r requirements.txt`\n    \nAfter installing and activating new environment (Note that the order is different \nin conda and Python) open IPython notebook\n\n`jupyter notebook MarineInvaders.ipynb`\n\nJupyter is part of Anaconda distribution. If the Python3.7 is used\nthen Jupyter must be installed in addition. For more information please refer to\n[Jupyter project](https://jupyter.readthedocs.io/en/latest/install.html).\n\n\n## Authors\nTODO\n\n## License\nThis project is licensed under The [3-Clause BSD License](LICENSE.md)",
    "bugtrack_url": null,
    "license": "GNU GPLv3",
    "summary": "The marinvaders (Marine Invaders) is tool to process data on marine invasive species from existing databases",
    "version": "0.0.8",
    "split_keywords": [],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "b7346433d02367701b958e1efc93bae4",
                "sha256": "516172a05198c514c816f44f5aca27ad983ff0ec129079f71832e1827881fb6d"
            },
            "downloads": -1,
            "filename": "marinvaders-0.0.8.tar.gz",
            "has_sig": false,
            "md5_digest": "b7346433d02367701b958e1efc93bae4",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.7.0",
            "size": 125601510,
            "upload_time": "2021-02-09T18:20:57",
            "upload_time_iso_8601": "2021-02-09T18:20:57.778076Z",
            "url": "https://files.pythonhosted.org/packages/fd/53/7203167c83b3e8fcd7799754d95907b6cee8252ffefc6b1683ef7c0cb346/marinvaders-0.0.8.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2021-02-09 18:20:57",
    "github": false,
    "gitlab": true,
    "bitbucket": false,
    "gitlab_user": null,
    "gitlab_project": "dlab-indecol",
    "lcname": "marinvaders"
}
        
Elapsed time: 0.19202s