ecospat.rangesize: Quantification of the range size of a species using habitat...

In ecospat: Spatial Ecology Miscellaneous Methods

Quantification of the range size of a species using habitat suitability maps and IUCN criteria)

Description

This function quantifies the range size of a species using standard IUCN criteria (Area of Occupancy AOO, Extent of Occurence EOO) or binary maps derived from Species Distribution Models.

Usage

ecospat.rangesize (bin.map, ocp, buffer, eoo.around.model, eoo.around.modelocp, 
xy, EOO, Model.within.eoo, AOO, resol, AOO.circles, d, lonlat, return.obj, 
save.obj, save.rangesize, directory)

ecospat.rangesize (bin.map = NULL,
                   ocp = TRUE,
                   buffer = 0,
                   eoo.around.model = TRUE,
                   eoo.around.modelocp = FALSE,
                   xy = NULL,
                   EOO = TRUE,
                   Model.within.eoo = TRUE,
                   AOO = TRUE,
                   resol = c(2000, 2000),
                   AOO.circles = FALSE,
                   d = sqrt((2000 * 2)/pi),
                   lonlat = FALSE,
                   return.obj = TRUE,
                   save.obj = FALSE,
                   save.rangesize = FALSE,
                   directory = getwd())

Arguments

bin.map	Binary map (a SpatRaster) from a Species Distribution Model.
ocp	logical. Calculate occupied patch models from the binary map (predicted area occupied by the species)
buffer	numeric. Calculate occupied patch models from the binary map using a buffer (predicted area occupied by the species or within a buffer around the species, for details see ?extract).
eoo.around.model	logical. The EOO around all positive predicted values from the binary map.
eoo.around.modelocp	logical. EOO around all positive predicted values of occupied patches.
xy	xy-coordinates of the species presence
EOO	logical. Extent of Occurrence. Convex Polygon around occurrences.
Model.within.eoo	logical. Area predicted as suitable by the model within EOO.
AOO	logical. Area of Occupancy ddervied by the occurrences.
resol	Resolution of the grid frame at which AOO should be calculated.
AOO.circles	logical. AOO calculated by circles around the occurrences instead of using a grid frame.
d	Radius of the AOO.circles around the occurrences.
lonlat	Are these longitude/latidue coordinates? (Default = FALSE).
return.obj	logical. should the objects created to estimate range size be returned (SpatRaster and spatial polygons). Default: TRUE
save.obj	logical. should objects be saved on hard drive?
save.rangesize	logical. should range size estimations be saved on hard drive .
directory	directory in which objects should be saved (Default = getwd())

Details

The range size of a species is important for many conservation purposes, e.g. to assess the status of threat for IUCN Red Lists. This function quantifies the range size using different IUCN measures, i.e. the Area Of Occupancy (AOO), the Extent Of Occurrence (EOO) and from binary maps derived from Species Distribution Models (SDMs). Different ways to extract range size from SDMs are available, e.g. using occupied patches, the suitable habitat within EOO or a convex hull around the suitable habitat.

Value

A list with the values of range size quantification and the stored objects used for quantification (of class SpatRaster, ahull, ConvexHull).

Author(s)

Frank Breiner [e-mail] with the contributions of Flavien Collart

References

IUCN. 2012. IUCN Red List Categories and Criteria: Version 3.1. Second edition. Gland, Switzerland and Cambridge, UK: IUCN. iv + 32pp.

IUCN Standards and Petitions Subcommittee. 2016. Guidelines for Using the IUCN Red List Categories and Criteria. Version 12. Prepared by the Standards and Petitions Subcommittee. Downloadable from http://www.iucnredlist.org/documents/RedListGuidelines.pdf

Pateiro-Lopez, B., and A. Rodriguez-Casal. 2010. Generalizing the Convex Hull of a Sample: The R Package alphahull. Journal of Statistical software, 34, 1-28.

See Also

ecospat.occupied.patch, ecospat.mpa, ecospat.binary.model

Examples

library(terra)
library(dismo)

# coordinates of the plots
xy <- ecospat.testData[,2:3]

# environmental data
predictors <- terra::rast(system.file("extdata","ecospat.testEnv.tif",package="ecospat"))
env <- terra::extract(predictors,xy,ID=FALSE)  
spData <- cbind.data.frame(occ=ecospat.testData$Veronica_alpina,env)
mod <- glm(occ~ddeg0+I(ddeg0^2)+srad68+I(srad68^2),data=spData,family = binomial())

# predict to entire dataset
pred <- terra::predict(predictors,mod,type="response") 
plot(pred)
points(xy[spData$occ==1,])
  
### make binary maps
#arbitratry threshold
pred.bin.arbitrary <- ecospat.binary.model(pred,0.3)
names(pred.bin.arbitrary) <- "me.arbitrary"
# use MPA to convert suitability to binary map
mpa.cutoff <- ecospat.mpa(pred,xy[spData$occ==1,])
pred.bin.mpa <- ecospat.binary.model(pred,mpa.cutoff)
names(pred.bin.mpa) <- "me.mpa"

### rangesize calculations

if(require(alphahull,quietly=TRUE)){

  rangesize2 <- ecospat.rangesize(c(pred.bin.mpa,pred.bin.arbitrary),
                                   xy=xy[spData$occ==1,],
                                   AOO.circles = TRUE,
                                   lonlat =FALSE)
  rangesize2$RangeSize
    
  names(rangesize2$RangeObjects)
    
  par(mfrow=c(1,3))
    
  plot(ecospat.binary.model(pred,0),legend=FALSE, main="IUCN criteria")
    
  ### IUCN criteria & derivates
    
  # plot AOO
  plot(rangesize2$RangeObjects$AOO,add=TRUE, col="red",legend=FALSE)
    
  # plot EOO
  plot(rangesize2$RangeObjects$EOO@polygons,add=TRUE, border="red", lwd=2)
    
  # plot circles around occurrences
  plot(rangesize2$RangeObjects$AOO.circle@polygons,add=TRUE,border="blue")
    
  for(i in 1:2){
    ## plot the occupied patches of the model
    plot(rangesize2$RangeObjects$models.ocp[[i]],col=c("grey","blue","darkgreen"),
          main=names(rangesize2$RangeObjects$models.ocp[[i]]),legend=FALSE)
    points(xy[spData$occ==1,],col="red",cex=0.5,pch=19)
    ## plot EOO around model
    plot(rangesize2$RangeObjects$eoo.around.model[[i]]@polygons,add=TRUE,border="blue",lwd=2)
    ## plot the modeled area within EOO
    #plot(rangesize$RangeObjects$model.within.eoo[[i]],col=c("grey","blue","darkgreen"))
    #points(occ,col="red",cex=0.5,pch=19)
    #plot(rangesize$RangeObjects$EOO@polygons,add=TRUE, border="red", lwd=2)
    }
  par(mfrow=c(1,1))
    
  ### Alpha-hulls are not included in the function yet because of Licence limitations.
  ### However, alpha-hulls can easily be included manually (see also the help file of 
  ### the alpha hull package):
    
  alpha = 2 # alpha value of 2 recommended by IUCN
    
  del<-alphahull::delvor(xy[spData$occ==1,])
  dv<-del$mesh
  mn <- mean(sqrt(abs(del$mesh[,3]-del$mesh[,5])^2+abs(del$mesh[,4]-del$mesh[,6])^2))*alpha
  alpha.hull<-alphahull::ahull(del,alpha=mn) 
    
  #Size of alpha-hulls
  #areaahull(alpha.hull) #works but uses a deprecated function in alphahull 2.1
    
  #plot alphahulls
  plot(rangesize2$RangeObjects$models.ocp[[1]],col=c("grey","blue","darkgreen"),
        main=names(rangesize2$RangeObjects$models.ocp[[1]]),legend=FALSE)
  plot(alpha.hull,add=TRUE,lwd=1)
}

ecospat documentation built on July 4, 2024, 5:06 p.m.