thrshld: Apply threshold for MaxEnt projections of a species

In HemingNM/ENMwizard: Advanced Techniques for Ecological Niche Modeling Made Easy

Apply threshold for MaxEnt projections of a species

Description

This function will apply the selected threshold criterias to MaxEnt model projection(s) of a 'mcmp' object and save on the folder "3_out.MaxEnt/Mdls.[species name]/Mdls.thrshld". For each projection (species and climatic scenario), two layers will be generated, one with suitability above the threshold value and another with presence/absence only.

Usage

thrshld(mcmp, thrshld.i = 4:6, t.all = FALSE, sp.nm = "species", numCores = 1)

Arguments

mcmp	An object returned by proj_mdl, containing calibrated models and model projections for each species; or species "i" of a object returned by "proj_mdl_b", containing a list of calibrated models and model projections for each species
thrshld.i	List of threshold criteria to be applied. Use numbers to choose the desired one(s). Current options: 1. Fixed.cumulative.value.1 (fcv1); 2. Fixed.cumulative.value.5 (fcv5); 3. Fixed.cumulative.value.10 (fcv10); 4. Minimum.training.presence (mtp); 5. 10.percentile.training.presence (x10ptp); 6. Equal.training.sensitivity.and.specificity (etss); 7. Maximum.training.sensitivity.plus.specificity (mtss); 8. Balance.training.omission.predicted.area.and.threshold.value (bto); 9. Equate.entropy.of.thresholded.and.original.distributions (eetd).
t.all	logical. Should threshold be applied on individual and consensus projections? Default is FALSE. Ignored if consensus projections are not found.
sp.nm	Species name. Used to name the output folder
numCores	Number of cores to use for parallelization. If set to 1, no paralellization is performed

Value

Stack or brick of thresholded predictions

See Also

thrshld_b

Examples

## Not run: 
mods.thrshld <- thrshld(mcmp=mxnt.mdls.preds, thrshld.i = 4:6)
plot(mods.thrshld[[1]][[2]]) # continuous
plot(mods.thrshld[[2]][[2]]) # binary

## End(Not run)

HemingNM/ENMwizard documentation built on Jan. 4, 2024, 3:24 p.m.