# NOT RUN {
library(raster)
spp <- ecospat.testNiche
xy.sp1<-subset(spp,species=="sp1")[2:3] #Bromus_erectus
load(system.file("extdata", "ecospat.testEnvRaster.Rdata", package="ecospat"))
#?ecospat.testEnvRaster
env.sp1<-extract(env,xy.sp1)
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
# 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,env)
plot(geoz1,main="z1")
points(xy.sp1)
# }
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