ade4: avijons – R documentation

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avijons

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)

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release