ecospat.niche.zProjGeo: Projection of Occurrence Densities to the Geography

In ecospat: Spatial Ecology Miscellaneous Methods

Projection of Occurrence Densities to the Geography

Description

Creates a raster in geography with each pixel containing the occurrence densities extracted from a z object generated with ecospat.grid.clim.dyn.

Usage

ecospat.niche.zProjGeo(z,zproj,env,cor)

Arguments

z	occurrence density grid created by ecospat.grid.clim.dyn.
zproj	NULL or occurrence density grid created by ecospat.grid.clim.dyn.
env	A SpatRaster of environmental variables corresponding to the background (glob1 in ecospat.grid.clim.dyn).
cor	FALSE by default. If TRUE corrects the occurrence densities of each species by the prevalence of the environments in their range

Details

extracts the occurrence density of z and project them in geography. If zproj=NULL, the occurrence density of z is extracted for each point of the background of z (glob1) using extract (package terra). The values are binded to the geographic coordinates of env and a raster is then recreated using rast with the argument type="xyz".If zproj is a occurrence density object, the background glob1 of this object is chosen and the projection is made on this background.env must then must be the same as used to create zproj.

Value

raster of class RasterLayer

Author(s)

Olivier Broennimann [e-mail]

References

Broennimann, O., M.C. Fitzpatrick, P.B. Pearman, B. Petitpierre, L. Pellissier, N.G. Yoccoz, W. Thuiller, M.J. Fortin, C. Randin, N.E. Zimmermann, C.H. Graham and A. Guisan. 2012. Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography, 21:481-497.

Petitpierre, B., C. Kueffer, O. Broennimann, C. Randin, C. Daehler and A. Guisan. 2012. Climatic niche shifts are rare among terrestrial plant invaders. Science, 335:1344-1348.

See Also

ecospat.plot.niche.dyn, ecospat.niche.dynIndexProjGeo

Examples

library(ade4)
library(terra)

data("ecospat.testNiche")
spp <- ecospat.testNiche
xy.sp1<-subset(spp,species=="sp1")[2:3] #Bromus_erectus

env<-terra::rast(system.file("extdata","ecospat.testEnv.tif",package="ecospat"))
#plot(env)

env.sp1<-terra::extract(env,xy.sp1)[,-1]
env.bkg<-na.exclude(terra::values(env))

#################################### PCA-ENVIRONMENT ##################################

pca.cal <- ade4::dudi.pca(env.bkg, center = TRUE, scale = TRUE, scannf = FALSE, nf = 2)

# predict the scores on the axes
scores.bkg <- pca.cal$li  #scores for background climate
scores.sp1 <- ade4::suprow(pca.cal,env.sp1)$lisup				#scores for sp1

# calculation of occurence density (niche z)
  
z1 <- ecospat.grid.clim.dyn(scores.bkg, scores.bkg, scores.sp1,R=100)

plot(z1$z.uncor)
points(scores.sp1)

#################################### occurrence density in space ##################################

# sp1
geoz1<-ecospat.niche.zProjGeo(z1,zproj=NULL,env=env)
plot(geoz1,main="z1")
points(xy.sp1)

ecospat documentation built on Oct. 18, 2023, 1:19 a.m.