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 of 6 components.

xy
  are the coordinates of 97 sites.
flo
  is a data frame with 97 sites and 56 species.
espnames
  is a vector of the names of species.
neig
  is the neighbourhood graph of the 97 sites (an object of class 'neig').
mil
  is a data frame with 97 sites and 11 environmental variables.
partition
  is a factor classifying the 97 sites in 5 classes.
area
  is a data frame of class `area`

### Source

Belair, G.d. 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.

### Examples

    data(mafragh)
    par(mfrow = c(3,2))
    s.label(mafragh$xy, inc = FALSE, neig = mafragh$neig,
        sub = "Samples & Neighbourhood graph")
    coa1 <- dudi.coa(mafragh$flo, scan = FALSE)
    s.value(mafragh$xy, coa1$li[,1], sub = "Axis 1 - COA")
    pca1 <- dudi.pca(mafragh$xy, scan = FALSE)
    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$area)
    neig1 <- neig(mat01 = 1*(link1>0))
    nb1 <- neig2nb(neig1)
    par(mfrow = c(2,1))
    area.plot(mafragh$area,center = mafragh$xy,clab=0.75)
    area.plot(mafragh$area,center = mafragh$xy,graph=neig1)
    if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
        lw1 <- apply(link1,1,function(x) x[x>0])
        listw1 <- nb2listw(nb1,lw1)
        coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4)
        ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0)
        summary(ms1)
        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)

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