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marinvaders

Marinvader - A python module for analysing alien and native marine species

MarINvaders: Full/alien species distributions for a single species or a whole ecoregion.

The is the entry point to the marINvaders code base providing the to top-level classes:

  • Species
  • MarinLife

For both, the algorithm collects species data from OBIS and connect to distribution of the species using WoRMS, NatCon and (optional) IUCN data sources. It uses geo-spatial regions based on MEOW ECOS merged with MRGID (used by WoRMS source) from different shape-files.

More about data processing can be found at README.md and documentation (https://marinvaders.gitlab.io/marinvaders/)

Classes
  • Species Class representing a single species.</>
  • MarineLife Class representing the marine life in selected MEOW eco-region.</>
Functions
  • marine_ecoregions(**kwargs) (geoPandas) Filter meow eco-regions using keywords arguments selectors.</>
  • plot(eco_code, show) (matplotlib plot figure) Plot world map with selected MEOW eco region</>

Requests to the web services APIs of OBIS and WORMS

OBIS: https://api.obis.org/ WoRMS: http://marinespecies.org/rest/

Functions
  • obis_taxon(aphia_ids) (DataFrame) Get extra fields from OBIS API using different url</>
  • request_obis(eco_code, aphia_id) (pandas.DataFrame) Query OBIS API either by marine ecoregion code or aphia_id. WhenTimeout error occurs the request is repeated 5 times.</>
  • request_worms(aphia_ids) (pandas DataFrame) Request call to WoRMS API web service</>

Utility module for reading different data sources.

Data sources are specified at README.md

Classes
Functions
  • data_path() (os.path) Path to data source files.</>
  • eco_mrgid_link() (pd.DataFrame) Reads ECO regions code from MEOW merged with other shapefiles. This file maps ECO regions code wit MRGID</>
  • read_gisd(gisd_file) (pd.DataFrame) Reads GISD dataset.</>
  • read_gisd_worms_link() (pd.DataFrame) Reads GISD and WoRMS qualitative distribution linked to MEOW.</>
  • read_natcon() (pd.DataFrame) Reads NatCon dataset.</>
  • read_redlist(redlist_file) (Pandas DataFrame) Reads redlist data which describes species affected by invasive species.</>
  • read_shapefile(shape_name) (GeoPandas) Read shapefiles.</>

Utiltiy module for finding observation for species.

The species reported by OBIS are used to search in WoRMS, GISD and NatCon observations sources and are merged if record was found as a alien means.

Functions
  • gisd(obis, gisd_file) (pandas.DataFrame) Process observations from GISD source.</>
  • natcon(obis) (pandas.DataFrame) Process observations for alien range from NatCon source.</>
  • observations(obis, species, gisd_file) (pd.DataFrame) Get the data from the available data sources.</>
  • worms(obis) (pandas.DataFrame) Process WoRMS observations for the specified species.</>