mafragh {ade4} | R Documentation |
This data set gives environmental and spatial informations about species and sites.
data(mafragh)
mafragh
is a list of 6 components.
are the coordinates of 97 sites.
is a data frame with 97 sites and 56 species.
is a vector of the names of species.
is the neighbourhood graph of the 97 sites (an object of class 'neig').
is a data frame with 97 sites and 11 environmental variables.
is a factor classifying the 97 sites in 5 classes.
is a data frame of class area
Belair, G.d. and Bencheikh-Lehocine, M. (1987) Composition et d?terminisme de la v?g?tation d'une plaine c?ti?re mar?cageuse : La Mafragh (Annaba, Alg?rie). Bulletin d'Ecologie, 18, 393–407.
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 = F) 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$area) neig1 <- neig(mat01 = 1*(link1 > 0)) nb1 <- neig2nb(neig1) if(adegraphicsLoaded()) { if(requireNamespace("sp", quiet = TRUE)) { g7 <- s.label(mafragh$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$xy, graph = neig1) par(mfrow = c(1, 1)) } if(requireNamespace("maptools", quiet = TRUE) & requireNamespace("spdep", quiet = TRUE)) { lw1 <- apply(link1, 1, function(x) x[x > 0]) listw1 <- nb2listw(nb1, lw1) coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4) ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0) summary(ms1) if(adegraphicsLoaded()) { if(requireNamespace("lattice", quiet = 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$as, plot = FALSE) g12 <- xyplot(ms1$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)) } } ## End(Not run)