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\name{avijons}
\alias{avijons}
\docType{data}
\title{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{
\code{avijons} is a list with the following objects :
\describe{
\item{xy}{: a data frame with the coordinates of the sites}
\item{area}{: an object of class \code{area}}
\item{fau}{: a data frame with the abundance of 64 bird species in 91 sites}
\item{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)
\emph{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. \emph{Environmental and Ecological Statistics}, \bold{2}, 1--14.
See a data description at \url{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)
\dontrun{
data(avijons)
if(!adegraphicsLoaded()) {
if(requireNamespace("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$li[, 2], pixmap = pnm.eau, inclu = FALSE,
grid = FALSE, addax = FALSE, cleg = 0, sub = "F2+WATER", csub = 3)
par(mfrow = c(1, 1))
}
if(requireNamespace("maptools", quiet = TRUE) & requireNamespace("spdep", quiet = TRUE) &
requireNamespace("pixmap", quiet = TRUE)) {
link1 <- area2link(avijons$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$li[, 1])
par(mfrow = c(1, 1))
par(mfcol = c(3, 2))
s.value(avijons$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))
}}}}
\keyword{datasets}
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