avijons {ade4}

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)