R: Phyto-Ecological Survey

mafragh {ade4} | R Documentation

## Phyto-Ecological Survey

### Description

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

neig

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

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.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))
      }
    }

    ## End(Not run)

[Package ade4 version 1.7-19 Index]