Phyto-Ecological Survey

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

Usage

data(mafragh)

Format

mafragh is a list with the following components:

xy

the coordinates of 97 sites

flo

a data frame with 97 sites and 56 species

env

a data frame with 97 sites and 11 environmental variables

partition

a factor classifying the 97 sites in 7 classes

area

a data frame of class area

tre

a character providing the phylogeny as a newick object

traits

a list of data frame. Each data frame provides the value of biological traits for plant species

nb

the neighbourhood graph of the 97 Mafragh sites (an object of class nb)

Spatial

the map of the 97 Mafragh sites (an object of the class SpatialPolygons of sp)

spenames

a data frame with 56 rows (species) and 2 columns (names)

Spatial.contour

the contour of the Magragh map (an object of the class SpatialPolygons of sp)

Source

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

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 = 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.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))
}


if (FALSE) { # \dontrun{
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) & requireNamespace("adespatial", 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 <- adespatial::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))
  }
}
} # }