Model algorithm: GBM
Explanatory variables: Bio4 (temperature seasonality), Bio5 (max temperature of warmest month), Bio12 (annual precipitation) and Bio15 (precipitation seasonality) were used for modelling birds and mammals. Bio4, Bio5, Bio18 (precipitation of warmest quarter) and Bio19 (precipitation of coldest quarter) were used for modelling amphibians.
Response variable: absence/presence of species
Additional information about response variable: Bio4 (temperature seasonality), Bio5 (max temperature of warmest month), Bio12 (annual precipitation) and Bio15 (precipitation seasonality) were used for modelling birds and mammals. Bio4, Bio5, Bio18 (precipitation of warmest quarter) and Bio19 (precipitation of coldest quarter) were used for modelling amphibians.
Parameters: n.trees=10500, n.minobsinnode = 10, interaction.depth=c(1,2,3), shrinkage=c(0.01, 0.001), bag.fraction=0.5
Additional information about parameters: Model performance was evaluated using cross-validation and the model parameters (combination of interaction.depth and shrinkage) that resulted in the lowest cross-validation error were used for the final model. Only models with an AUC of > 0.7 were kept as results.
Software function: gbm()
Software package: gbm
Software program: R
Additional information about model output: The model output is the probability of occurrence of a species, which can vary between 0 and 1 (see for example amphibian-prob output files). Note: Probability of occurrence is projected to the present and all neighbouring realms of a species and so sort of represents the unlimited dispersal of a species in the future.
The output (probability of occurrence) of all species is then stacked (added up) to a summed probability of occurrence (a proxy of species richness) for (i) all species, (ii) all endemic species and (iii) all threatened species of the three modelled vertebrate taxa (see for example amphibian-sum-prob output files). Summed probability of occurrence is split into different dispersal scenarios (no dispersal, d/2, d, 2*d, full dispersal). Full dispersal represents the sum of the probability of occurrence output files. No dispersal assumes that species can only be present where they are actually present according to the IUCN and BirdLife range maps. The other three dispersal scenarios consider species-specific dispersal buffers added to the present range, where d is the largest diameter of the original range of the species.