ade4 (version 1.7-5)

mafragh: Phyto-Ecological Survey

Description

This data set gives environmental and spatial informations about species and sites.

Usage

data(mafragh)

Format

mafragh is a list of 6 components.

Source

de Belair, G. and Bencheikh-Lehocine, M. (1987) Composition et déterminisme de la végétation d'une plaine côtière marécageuse : La Mafragh (Annaba, Algérie). Bulletin d'Ecologie, 18, 393--407. Pavoine, S., Errol, V., Gaschet, S., De Belair, 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, In press.

References

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps053.pdf (in French).

Examples

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)