2023-02-05
Outline
Diagram
R Package for Workflow
SDMWorkflows
- No current package has all the tools for our workflow
- Cleaner way in one package
- SDMWorkflows
Taxonomic resolver
Taxonomic resolver (Ready!)
- Extract all taxons from arter.dk
- Resolve Synonyms and other probelems within
SDMWorkflows
- Function
Clean_Taxa
, already tested
- Being tested by ecogenetics
- Started with 60,958 taxa, ended with 40,328 species
Climatic downscaling
Climtatic Downscaling
- Based on Chelsa Downscaling to 10 mts
- Repo with code ready
- Need help with Python code (Zsofia, Ollie, Donjeta)
- Quick and dirty alternative
Storage challenges
- At least 4 scenarios
- Monthly max, min temp and prec
- 2000 to 2100
- Generate bioclimatic variables but try to get drought indices
- 4 Scenarios x 100 years x 12 months x 3 variables
14,400 rasters
Alternatives
Presence cleaning
Solved
- Centroid detection
- Spatial outlayers
- Temporal outlayers
Our bottleneck (Spatial thinning)
- Priorly working with the spThin package
- It has now clear way of establishing thinning distance
- Very slow for species with large numbers
- Maximizes number of presences in rare species
- Minimizing morans I for threshold
- Faster algorithm for more common species
- Limit maximum presences (1000?)
SDM
Maxent
- Only one with presence only (no pseudoabsences)
- Just try several settings and solve throuhg AICc or TSS
- Store models
Projections
Data volume
- 40,328 x 4 scenarios x 4 timesteps
645,248 rasters
- For know Cloud Optimized Geotiffs