Vegetation in Trois-Fontaines
This data set contains abundance values (Braun-Blanquet scale) of 80 plant species for 337 sites. Data have been collected by Sonia Said and Francois Debias.
data(vegtf)
vegtf is a list with the following components:
a data.frame with the abundance values of 80 species (columns) in 337 sites (rows)
a data.frame with the spatial coordinates of the sites
a data.frame (area) which define the boundaries of the study site
a vector containing the species latin names
a neighborhood object (class nb defined in package spdep)
an object of the class SpatialPolygons of sp,
containing the map
Dray, S., Said, S. and Debias, F. (2008) Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation. Journal of vegetation science, 19, 45–56.
if(requireNamespace("spdep", quietly = TRUE)) {
data(vegtf)
coa1 <- dudi.coa(vegtf$veg, scannf = FALSE)
ms.coa1 <- multispati(coa1, listw = spdep::nb2listw(vegtf$nb), nfposi = 2,
nfnega = 0, scannf = FALSE)
summary(ms.coa1)
plot(ms.coa1)
if(adegraphicsLoaded()) {
g1 <- s.value(vegtf$xy, coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = FALSE)
g2 <- s.value(vegtf$xy, ms.coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = FALSE)
g3 <- s.label(coa1$c1, plot = FALSE)
g4 <- s.label(ms.coa1$c1, plot = FALSE)
G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
} else {
par(mfrow = c(2, 2))
s.value(vegtf$xy, coa1$li[, 1], area = vegtf$area, include.origin = FALSE)
s.value(vegtf$xy, ms.coa1$li[, 1], area = vegtf$area, include.origin = FALSE)
s.label(coa1$c1)
s.label(ms.coa1$c1)
}
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