Species Spaces

Using shape files from IUCN database to determine habitat area (km²) for a given species.

made by Abby Criswell with the Havird Lab at the University of Texas at Austin updated 10-2-2023

Dependencies:

• python
• geopandas 0.13.2 +

To Use:

1. download SpatialDatafromShapefiles.py
2. setup dependencies [I recommend using pip: https://geopandas.org/en/stable/getting_started/install.html#installing-with-pip)]
3. gather folder containing folders (name: species) with shapefile (1 per species, name: 'data_0.shp') [This should be the default file structure when downloading shapefiles from IUCN.] [Example: For the species Bufo japonicus, need the file Data_Folder/Bufo japonicus/data_0.shp. See example files in repository.]
4. gather list of species to process as a tsv file (defaults to not reading first line for column headers) [See the example file 'specieslist.tsv' in repository.]
5. change path variables in SpatialDatafromShapefiles.py
   • path: where output should be put [Example: "./Example/" puts output as shown in example files in repository.]
   • shapefile_path: folder containing shapefile folders (labeled by species) [Example: "./Example/Data_Folder/" takes in shapefiles as shown in example files in repository.]
   • specieslist_path: path to csv file with list of species to try [Example: "./Example/specieslist.tsv" reads list file as shown in example files in repository.]
6. change range types of interest variable in SpatialDatafromShapefiles.py
   • range_types_of_interest: list of types of ranges to include in the area calculation
   • choose from the default groups of types provided or make a custom list of types)
   • defaults provided:
     • historical range: includes extant and extinct resident and breeding areas (includes reintroducted and origin uncertain, but not introduced, non-breeding, vagrant, or passage)
     • current range: includes extant resident and breeding areas (includes introduced, reintroduced, possibly extinct, and origin uncertain, but not extinct, non-breeding, vagrant, or passage)
     • total range: includes all types of ranges
7. run SpatialDatafromShapefiles.py
   • can do this by navigating to this file in terminal and using this command: python SpatialDatafromShapefiles.py
8. output:
   • Species area results listed in 'species_info.tsv' [See the example file 'species_info.tsv' in repository.]
   • If analysis for a species was unsuccessful (data missing, mislabeled, computation error), listed in 'species_notfound.txt' [See the example file 'species_info.tsv' in repository.]

Thank you to IUCN for data used in analysis.