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 12 components:

xy

are the coordinates of 97 sites.

flo

is a data frame with 97 sites and 56 species.

neig

is the neighbourhood graph of the 97 sites (an object of class neig).

env

is a data frame with 97 sites and 11 environmental variables.

partition

is a factor classifying the 97 sites in 7 classes.

area

is 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

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

Spatial

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

spenames

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

Spatial.contour

is 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.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("maptools", quietly = TRUE) & 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))
  }
}

## End(Not run)