Phyto-Ecological Survey
This data set gives environmental and spatial informations about species and sites.
data(mafragh)
mafragh is a list with the following components:
the coordinates of 97 sites
a data frame with 97 sites and 56 species
the neighbourhood graph of the 97 sites (an object of class neig)
a data frame with 97 sites and 11 environmental variables
a factor classifying the 97 sites in 7 classes
a data frame of class area
a character providing the phylogeny as a newick object
a list of data frame. Each data frame provides the value of biological traits for plant species
the neighbourhood graph of the 97 Mafragh sites (an object of class nb)
the map of the 97 Mafragh sites (an object of the class SpatialPolygons of sp)
a data frame with 56 rows (species) and 2 columns (names)
the contour of the Magragh map (an object of the class SpatialPolygons of sp)
de Bélair, Gérard and Bencheikh-Lehocine, Mahmoud (1987) Composition et déterminisme de la végétation d'une plaine côtière marécageuse : La Mafragh (Annaba, Algérie). Bulletin d'Ecologie, 18(4), 393–407.
Pavoine, S., Vela, E., Gachet, S., de Bélair, G. and Bonsall, M. B. (2011) Linking patterns in phylogeny, traits, abiotic variables and space: a novel approach to linking environmental filtering and plant community assembly. Journal of Ecology, 99, 165–175. doi:10.1111/j.1365-2745.2010.01743.x
See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps053.pdf (in French).
data(mafragh)
coa1 <- dudi.coa(mafragh$flo, scan = FALSE)
pca1 <- dudi.pca(mafragh$xy, scan = FALSE)
if(adegraphicsLoaded()) {
g1 <- s.label(mafragh$xy, nb = mafragh$nb, psub.text = "Samples & Neighbourhood graph",
plot = FALSE)
g2 <- s.value(mafragh$xy, coa1$li[, 1], psub.text = "Axis 1 - COA", plot = FALSE)
g3 <- s.value(mafragh$xy, pca1$li[, 1], psub.text = "Axis 1 - PCA", plot = FALSE)
g4 <- s.class(pca1$li, mafragh$partition, psub.text = "Plane 1-2 - PCA", plot = FALSE)
g5 <- s.class(coa1$li, mafragh$partition, psub.text = "Plane 1-2 - COA", plot = FALSE)
g6 <- s.class(mafragh$xy, mafragh$partition, chullSize = 1, ellipseSize = 0, starSize = 0,
ppoints.cex = 0, plot = FALSE)
G <- ADEgS(c(g1, g2, g3, g4, g5, g6), layout = c(3, 2))
} else {
par(mfrow = c(3, 2))
s.label(mafragh$xy, inc = FALSE, neig = mafragh$neig, sub = "Samples & Neighbourhood graph")
s.value(mafragh$xy, coa1$li[, 1], sub = "Axis 1 - COA")
s.value(mafragh$xy, pca1$li[, 1], sub = "Axis 1 - PCA")
s.class(pca1$li, mafragh$partition, sub = "Plane 1-2 - PCA")
s.class(coa1$li, mafragh$partition, sub = "Plane 1-2 - COA")
s.chull(mafragh$xy, mafragh$partition, optchull = 1)
par(mfrow = c(1, 1))
}
## Not run:
link1 <- area2link(mafragh$area)
neig1 <- neig(mat01 = 1*(link1 > 0))
nb1 <- neig2nb(neig1)
if(adegraphicsLoaded()) {
if(requireNamespace("sp", quietly = TRUE)) {
g7 <- s.label(mafragh$xy, Sp = mafragh$Spatial, pSp.col = "white", plot = FALSE)
g8 <- s.label(mafragh$xy, Sp = mafragh$Spatial, pSp.col = "white", nb = nb1, plab.cex = 0,
pnb.node.cex = 0, ppoints.cex = 0, plot = FALSE)
G <- ADEgS(c(g7, g8), layout = c(2, 1))
}
} else {
par(mfrow = c(2, 1))
area.plot(mafragh$area, center = mafragh$xy, clab = 0.75)
area.plot(mafragh$area, center = mafragh$xy, graph = neig1)
par(mfrow = c(1, 1))
}
if(requireNamespace("spdep", quietly = TRUE)) {
lw1 <- apply(link1, 1, function(x) x[x > 0])
listw1 <- spdep::nb2listw(nb1, lw1)
coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4)
ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0)
summary(ms1)
if(adegraphicsLoaded()) {
if(requireNamespace("lattice", quietly = TRUE)) {
g9 <- s1d.barchart(coa1$eig, p1d.hori = FALSE, plot = FALSE)
g10 <- s1d.barchart(ms1$eig, p1d.hori = FALSE, plot = FALSE)
g11 <- s.corcircle(ms1$as, plot = FALSE)
g12 <- lattice::xyplot(ms1$li[, 1] ~ coa1$li[, 1])
G <- ADEgS(list(g9, g10, g11, g12), layout = c(2, 2))
}
} else {
par(mfrow = c(2, 2))
barplot(coa1$eig)
barplot(ms1$eig)
s.corcircle(ms1$as)
plot(coa1$li[, 1], ms1$li[, 1])
par(mfrow = c(1, 1))
}
}
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