Calculates the rarity index as defined in https://mdata.mnhn.lu/include/mai/NuL10-17-325-333-Ott.pdf on the Luxembourgish territory. If you want to use it in other regions, you need to adapt the grid cell generation in haeufindex.sql.
apt install sqlite3 spatialite-bin
- Export a csv file from https://mdata.mnhn.lu/ that includes all obeservations of a reference taxon in a reference time. Alternatively it reads any csv file that has a 'Long', 'Lat', 'Taxon_Kingdom', 'Taxon_Phylum', 'Taxon_Class', 'Taxon_Order', 'Taxon_Family', 'Taxon_Genus' and 'preferred' (the taxon name) colum.
- Install dependencies
- Check out this repository using git
- Change into git repository
- Download a bounding shape file and extract here (eg. limadmin-shp.zip from https://data.public.lu/en/datasets/limites-administratives-du-grand-duche-de-luxembourg/). Also adjust the bounding box in
haeufindex.sqlif the analysis is to be run on another region than the country Luxembourg. - Run
sh haeufindex.sh observations.csv output.csv 1000 LIMADM_PAYS familyfor an analysis on 1km squares bounded by the LIMADM_PAYS.[shp,shx,dbf,prj] shapefile relative to the taxon levelfamily. - Read the output in the file
output.csv
Note: If you want to do additional analysis, you can run spatialite /tmp/loaded.sqlite after running the analysis. This database contains the following interesting tables:
- obs_norm: observations with reference to cell they are contained in
- aai, agi, ami: The components of mAI
- mai: The results