NESP Threatened Species Recovery Hub Project 8.3.1: ‘Fire-affected invertebrates: priority species and management response’.

Team

John Woinarski, Libby Rumpff, Jess Marsh, Payal Bal

Collaborators

August Hao - data cleaning discussions and scripts
Lee Belbin, Matilda Stevenson – ALA data cleaning discussions and advice on ala4R
Casey Visitin – Collaborator on overlap script using gdal functions
Darren Southwell, Diego Brizuela Torres, David Wilkinson – SDMs for priority invertebrates

Data

https://zenodo.org/record/5091296#.ZD4bTxVBzao

Contact author

payal.bal@unimelb.edu.au

Workflow in Rscripts

1. Cleaning AFD checklist: https://github.com/payalbal/nesp_bugs/blob/master/scripts/splist_AFD.R
   

• Function to remove improper names: https://github.com/payalbal/nesp_bugs/blob/master/scripts/remove_improper_names.R
  

2. Download ALA data by phyla: https://github.com/payalbal/nesp_bugs/blob/master/scripts/download_ALA_bytaxon.R
   

• Function to download data by phyla: https://github.com/payalbal/nesp_bugs/blob/master/scripts/get_ala_taxondata.R
  

To download ALA data by species: https://github.com/payalbal/nesp_bugs/blob/master/scripts/download_ALA_byspecies.R

• Function to download data by species: https://github.com/payalbal/nesp_bugs/blob/master/scripts/get_ala_spdata.R
  

3. ALA processing script: https://github.com/payalbal/nesp_bugs/blob/master/scripts/ala_processing1.R
   

• Function to remove improper names: https://github.com/payalbal/nesp_bugs/blob/master/scripts/remove_improper_names.R
  
• Function to find name source and habitat information (author: Matilda Stevenson, ALA): https://github.com/payalbal/nesp_bugs/blob/master/scripts/get_source.R (uses ALA4R function under dev called ala_taxa())
  
• Function to find AFD synonyms for species names: https://github.com/payalbal/nesp_bugs/blob/master/scripts/get_AFDsynonyms.R
  

4. Summary script for cleaned ALA data: https://github.com/payalbal/nesp_bugs/blob/master/scripts/ala_summary.R
   

5. Create mask from QGIS output: https://github.com/payalbal/nesp_bugs/blob/master/scripts/ausmask.R
   

6. Format, combine and clean individual non-ALA datasheets: https://github.com/payalbal/nesp_bugs/blob/master/scripts/nonala_processing.R
   

7. Combine ALA and non-ALA data and format data table: https://github.com/payalbal/nesp_bugs/blob/master/scripts/data_ALAnonALA.R
   

8. Correcting species name & updating ALAnonALA data: https://github.com/payalbal/nesp_bugs/blob/master/scripts/data_correction_speciesnames.R
   

9. Create polygons using IUCN.eval() function from ConR package for all data: https://github.com/payalbal/nesp_bugs/blob/master/scripts/species_polygons.R
   

• Function based on IUCN.eval() function from ConR package: https://github.com/payalbal/nesp_bugs/blob/master/scripts/conr_iucn_eval.R
  
• To convert alpha hulls in the .rds file into shapefiles: https://github.com/payalbal/nesp_bugs/blob/master/scripts/rds_to_shp_conversion.R
  

10. Prepare regional layers: https://github.com/payalbal/nesp_bugs/blob/master/scripts/regions.R
    

11. Region overlaps: https://github.com/payalbal/nesp_bugs/blob/master/scripts/species_regionoverlap.R
    

• Region overlap function: https://github.com/payalbal/nesp_bugs/blob/master/scripts/region_overlap.R
  

12. Prepare GEEBAM fire severity layer: https://github.com/payalbal/nesp_bugs/blob/master/scripts/firemap.R
    

13. For full extent including offland islands and territories: https://github.com/payalbal/nesp_bugs/blob/master/scripts/firemap_ausextent.R
    

14. Fire overlap for all species with point data: https://github.com/payalbal/nesp_bugs/blob/master/scripts/species_points_fireoverlap.R
    

• Points overlap function: https://github.com/payalbal/nesp_bugs/blob/master/scripts/points_overlap.R
  

15. Fire overlap for species with polygons: https://github.com/payalbal/nesp_bugs/blob/master/scripts/species_EOO_fireoverlap_paa.R
    

• Polygon overlap function: https://github.com/payalbal/nesp_bugs/blob/master/scripts/polygon_paa_overlap.R
  

16. Combine polygon and point output table: https://github.com/payalbal/nesp_bugs/blob/master/scripts/fireoverlap_table_withPAA.R
    

17. Aquatic species overlaps: https://github.com/payalbal/nesp_bugs/blob/master/scripts/aquatic_inverts.R
    

• Slugrisk point overlap function: https://github.com/payalbal/nesp_bugs/blob/master/scripts/points_slugrisk_overlap.R
  
• Slugrisk polygon overlap function: https://github.com/payalbal/nesp_bugs/blob/master/scripts/polygon_slugrisk_overlap.R