R: Bird species distribution

avijons {ade4} | R Documentation

## Bird species distribution

### Description

This data set contains information 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 components:

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

Spatial

  an object of the class `SpatialPolygons` of `sp`, containing the map

### 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.

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps051.pdf (in French).

### 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(!adegraphicsLoaded()) {
      if(requireNamespace("pixmap", quietly = TRUE)) {
        pnm.eau <- pixmap::read.pnm(system.file("pictures/avijonseau.pnm", package = "ade4"))
        pnm.rou <- pixmap::read.pnm(system.file("pictures/avijonsrou.pnm", package = "ade4"))
        pnm.veg <- pixmap::read.pnm(system.file("pictures/avijonsveg.pnm", package = "ade4"))
        pnm.vil <- pixmap::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(requireNamespace("spdep", quietly = TRUE) &
        requireNamespace("pixmap", quietly = TRUE)) {

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

[Package ade4 version 1.7-18 Index]