ecospat.niche.dynIndexProjGeo: Projection of niche dynamic indices to the Geography

In ecospat: Spatial Ecology Miscellaneous Methods

Projection of niche dynamic indices to the Geography

Description

Creates a SpatRaster in geography with each pixel containing a niche dynamic index (stability, expansion, or unfilling) extracted from 2 niches generated with ecospat.grid.clim.dyn.

Usage

ecospat.niche.dynIndexProjGeo(z1, z2, proj, env)

Arguments

z1	Species 1 occurrence density grid created by ecospat.grid.clim.dyn.
z2	Species 2 occurrence density grid created by ecospat.grid.clim.dyn.
proj	type of projection (0,1 or 2)
env	A SpatRaster of environmental variables corresponding to the background (glob in ecospat.grid.clim.dyn).

Details

Extracts the niche dynamic index of objects created by ecospat.niche.dyn.index for each background point (glob) using extract from the terra package. The values are projected to the geographic coordinates of env and returned as a SpatRaster layer. If proj=0, the common background for z1 and z2 (glob) is used. If proj=1, the background (glob1) of z1 is used. If proj=2, the background (glob1) of z2 is used.

Value

a SpatRaster with cell values 0-3. 1: unfilling (habitat occupied by species 1); 2: expansion (habitat occupied only by species 2); 3: stability (habitat occupied by both species); and 0 (unoccupied habitat).

Author(s)

Olivier Broennimann [e-mail], Tyler Smith [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.dyn.index, ecospat.niche.zProjGeo

Examples

library(ade4)
library(terra)

data(ecospat.testNiche)
spp <- ecospat.testNiche
xy.sp1 <- subset(spp, species=="sp1")[2:3] #Bromus_erectus
xy.sp2 <- subset(spp, species=="sp4")[2:3] #Pritzelago_alpina

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

env.sp1 <- terra::extract(env, xy.sp1)[,-1]
env.sp2 <- terra::extract(env, xy.sp2)[,-1]
env.bkg <- na.exclude(terra::values(env))

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

library(ade4)
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
scores.sp2 <- ade4::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, pch = 21, bg = "green")

plot(z2$z.uncor)
points(scores.sp2, pch = 21, bg = "red")

ecospat.plot.niche.dyn(z1, z2)
points(scores.sp1, pch = 21, bg = "green")
points(scores.sp2, pch = 21, bg = "red")
ecospat.niche.overlap(z1,z2 ,cor = TRUE)

##############################
## dynamic indices in space ##
##############################

geozS <- ecospat.niche.dynIndexProjGeo(z1, z2, proj=0, env)

plot(geozS, col = c("grey", "green", "red", "blue"),
     legend = FALSE)
points(xy.sp1, bg = "green", pch = 21)
points(xy.sp2, bg = "red", pch = 21)

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