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n2kEvalSDM

This code is for modelling, projecting and evalutating species distribution models for 41 tree species. The code is written for use on a slurm HPC but should be runnable on a desktop machine. Change arguments according to the R script you want to run.

The orchestrateSpecies.sh is starting various R scripts for

  • separating into spatial blocks (blockSeparation.r)
  • modelling (modelling.r)
  • predicting (prediction.r)
  • evaluating for Natura 2000 areas (compare.r)

Spatial blocking

  • uncomment blockSeparation.r in orchestrateSpecies.sh
  • run bash orchestrateSpecies.sh in terminal

Modelling

  • Change model accroding to the one you want to run in orchestrateSpecies.sh
  • uncomment modelling.r
  • run bash orchestrateSpecies.sh in terminal

Prediction

  • uncomment prediction.r in orchestrateSpecies.sh
  • run bash orchestrateSpecies.sh in terminal

Evaluating species dstribution changes for Natura 2000 sites

  • uncomment compare.r in orchestrateSpecies.sh
  • keep "ABC" or change to either or if you want to evaluate for only Birds (A) or Habitats Directive (B) or both (C) areas
  • run bash orchestrateSpecies.sh in terminal

In all codes the paths are changed. So please chnage paths in all files according to your preferences.