ade4 (version 1.2-2)

avijons: Bird species distribution

Description

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

Usage

data(avijons)

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 propri�t�s des �cocomplexes de la plaine du Rh�ne : descripteurs de fonctionnement global et gestion des berges. Rapport programme S.R.E.T.I.E., Minist�re 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)
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))
}