# NOT RUN {
library(raster)
data(ecospat.testNiche)
spp <- ecospat.testNiche
xy.sp1<-subset(spp,species=="sp1")[2:3] #Bromus_erectus
xy.sp2<-subset(spp,species=="sp3")[2:3] #Daucus_carota
load(system.file("extdata", "ecospat.testEnvRaster.Rdata", package="ecospat"))
env.sp1<-extract(env,xy.sp1)
env.sp2<-extract(env,xy.sp2)
env.bkg<-na.exclude(values(env))
#################################### PCA-ENVIRONMENT ##################################
pca.cal <- dudi.pca(env.bkg, center = TRUE, scale = TRUE, scannf = FALSE, nf = 2)
# predict the scores on the axes
scores.bkg <- pca.cal$li #scores for background climate
scores.sp1 <- suprow(pca.cal,env.sp1)$lisup #scores for sp1
scores.sp2 <- suprow(pca.cal,env.sp2)$lisup #scores for sp2
# calculation of occurence density (niche z)
z1 <- ecospat.grid.clim.dyn(scores.bkg, scores.bkg, scores.sp1,R=100)
z2 <- ecospat.grid.clim.dyn(scores.bkg, scores.bkg, scores.sp2,R=100)
plot(z1$z.uncor)
points(scores.sp1)
plot(z2$z.uncor)
points(scores.sp2)
ecospat.niche.overlap(z1,z2 ,cor = TRUE)
#################################### stability S in space ##################################
geozS<-ecospat.niche.dynIndexProjGeo(z1,z2,env,index="stability")
plot(geozS,main="Stability")
points(xy.sp1,col="red")
points(xy.sp2,col="blue")
# }
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