avijons {ade4} | R Documentation

## Bird species distribution

### Description

This data set contains informations about spatial distribution of bird species in a zone surrounding the river Rhône near Lyon (France).

### Usage

    data(avijons)

### Format

`avijons` is a list with the following objects :

xy
  : a data frame with the coordinates of the sites
area
  : an object of class `area`
fau
  : a data frame with the abundance of 64 bird species in 91 sites
spe.names.fr
  : a vector of strings of character with the species names in french

### Source

Bournaud, M., Amoros, C., Chessel, D., Coulet, M., Doledec, S., Michelot, J.L., Pautou, G., Rostan, J.C., Tachet, H. and Thioulouse, J. (1990) Peuplements d'oiseaux et propriétés des écocomplexes de la plaine du Rhône : descripteurs de fonctionnement global et gestion des berges. Rapport programme S.R.E.T.I.E., Ministère de l'Environnement CORA et URA CNRS 367, Univ. Lyon I.

### References

Thioulouse, J., Chessel, D. and Champely, S. (1995) Multivariate analysis of spatial patterns: a unified approach to local and global structures. Environmental and Ecological Statistics, 2, 1–14.

### Examples

    data(avijons)
    w1=dudi.coa(avijons$fau,scannf=FALSE)$li
    area.plot(avijons$area,center=avijons$xy,val=w1[,1],clab=0.75,sub="CA Axis 1",csub=3)
    ## Not run:
    data(avijons)
    if (require(pixmap,quiet=TRUE)) {
        pnm.eau <- read.pnm(system.file("pictures/avijonseau.pnm",
            package = "ade4"))
        pnm.rou <- read.pnm(system.file("pictures/avijonsrou.pnm",
            package = "ade4"))
        pnm.veg <- read.pnm(system.file("pictures/avijonsveg.pnm",
            package = "ade4"))
        pnm.vil <- read.pnm(system.file("pictures/avijonsvil.pnm",
            package = "ade4"))
        jons.coa <- dudi.coa(avijons$fau, scan = FALSE, nf = 4)
        par(mfcol = c(3,2))
        s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.rou, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+ROADS", csub = 3)
        s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.veg, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+TREES", csub = 3)
        s.value(avijons$xy, jons.coa$li[,1], pixmap = pnm.eau, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+WATER", csub = 3)
        s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.rou, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+ROADS", csub = 3)
        s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.veg, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+TREES", csub = 3)
        s.value(avijons$xy, jons.coa$li[,2], pixmap = pnm.eau, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+WATER", csub = 3)
    par(mfrow=c(1,1))}

    if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)
            & require( pixmap, quiet = TRUE) ) {
        link1 <- area2link(avijons$area)
        lw1 <- apply(link1,1,function(x) x[x>0])
        neig1 <- neig(mat01=1*(link1>0))
        nb1 <- neig2nb(neig1)
        listw1 <- nb2listw(nb1,lw1)
        jons.ms <- multispati(jons.coa, listw1, scan = FALSE, nfp = 3,
         nfn = 2)
        summary(jons.ms)
        par(mfrow = c(2,2))
        barplot(jons.coa$eig)
        barplot(jons.ms$eig)
        s.corcircle(jons.ms$as)
        plot(jons.coa$li[,1], jons.ms$li[,1])

        par(mfcol=c(3,2))
        s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.rou, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+ROADS", csub = 3)
        s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.veg, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+TREES", csub = 3)
        s.value(avijons$xy, jons.ms$li[,1], pixmap = pnm.eau, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F1+WATER", csub = 3)
        s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.rou, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+ROADS", csub = 3)
        s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.veg, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+TREES", csub = 3)
        s.value(avijons$xy, jons.ms$li[,2], pixmap = pnm.eau, inclu = FALSE,
        grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+WATER", csub = 3)
    par(mfrow=c(1,1))
    }## End(Not run)

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