Code for the generation of a venomous snake species vulnerability surface, identifying populations at risk of exposure to venomous snake species. Project is currently in progress. Main themes of the project:
- Digitise existing expert opinion range maps for all medically important venomous snake species
- Provide recommendations for contemporary updates to the range of each of these species
- Create a contemporary medically important venomous snake distribution surface, classified by medical importance classification
- Compare this species distribution surface with population distribution, health care quality and accessibility, antivenom availability and travel time to health care data to identify the most vulnerable populations.
Expert opinion range (EOR) maps for medically important snake species were obtained from the WHO antivenom database (http://apps.who.int/bloodproducts/snakeantivenoms/database/). Each EOR map was digitized, and a shapefile was created for each unique species per map. Utilizing the spocc package, available species occurrence data was obtained for each species (n = 277). This species occurrence data was used to generate Multivariate Environmental Similarity Surface (MESS) for each species, highlighting locations which are environmentally similar to locations within the species occurrence data. These MES surfaces were then used to validate any occurrence data located outside of the currently accepted EOR, and to inform a process generating an amended, contemporary species range.
The newly created ranges were then converted to raster format, and stacked to generate a surface identifying the global range of medically important venomous snake species. This surface was combined with population distribution information, a ranking of health care quality and accessibility (HAQ Index), antivenom availability, and travel time to urban centers to identify the most vulnerable populations.
Broad overview of the project workflow. Each stage refers to a specific script within this repository.
- get_who_snakes.R: This script bulk downloads EOR maps from the WHO antivenom database, and converts these downloaded maps into PNG fomat to allow georeferencing and digitization in ArcMAP.
- plot_occurrence_spocc.R: This script cycles through each medically important venomous snake species and downloads available occurrence records from the online repositories GBIF, VertNet, iNaturalist, iDigBio and Ecoengine utilizing the
spoccpackage (https://CRAN.R-project.org/package=spocc). This occurrence data was then overlaid on top of digitized range shapefiles to show the distribution of occurrence records for each species. - gen_mess_cluster.R: This script utilizes the occurrence data obtained in the step above, and generates a Multivariate Environmental Similarity Surface (MESS) for each species. The MESS is constructed using occurrence records within the species' currently accepted EOR. The MESS is then used to evaluate occurrence records which are located outside of the currently accepted EOR. Records outside of the EOR, which are within interpolation space (MESS +ve) are used to create an amended, proposed range. This range is generated by buffering MESS +ve records by 100km (tbc), and clipping the buffered areas by the MESS interpolation space.
- convert_shp_to_raster.R: This script converts the newly generated/modified ranges to raster format. If a species has no range modification, the original WHO EOR is rasterized. Separate rasters are created for Category 1, Category 2 and combined C1 and C2 species.
- gen_species_richness.R: This script loops through the species rasters, and creates a raster stack. Cell values across the stack are then summed to give a count of the number of medically important venomous snake species per cell. This process is performed to generate separate Category 1, Category 2 and combined C1 and C2 species richness surfaces.
- gen_antivenom_coverage.R: This script loops through each species and groups species whose envenomings can be treated using the same antivenom. Using the species' range, a surface is generated to show the maximal spatial extent of efficacy for each antivenom. This script utilizes antivenom data from the WHO antivenom database.