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 objects :

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

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/pps/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 (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))
}
## End(Not run)

Worked out examples


> library(ade4)
> ### Name: avijons
> ### Title: Bird species distribution
> ### Aliases: avijons
> ### Keywords: datasets
> 
> ### ** 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))
+ }
deldir 0.0-12 

     Please note: The process for determining duplicated points
     has changed from that used in version 0.0-9 (and previously).


Multivariate Spatial Analysis
Call: multispati(dudi = jons.coa, listw = listw1, scannf = FALSE, nfposi = 3, 
    nfnega = 2)

Scores from the initial duality diagramm:
          var       cum      ratio      moran
RS1 0.3285555 0.3285555 0.08159205 0.37450880
RS2 0.2734770 0.6020325 0.14950613 0.10877438
RS3 0.2535429 0.8555754 0.21246988 0.03275436
RS4 0.2341904 1.0897658 0.27062772 0.33518157

Multispati eigenvalues decomposition:
             eig       var      moran
CS1   0.19270364 0.2706790  0.7119267
CS2   0.12951012 0.2140994  0.6049065
CS3   0.08762867 0.1748095  0.5012809
CS62 -0.05365942 0.1419862 -0.3779199
CS63 -0.07429149 0.1730170 -0.4293883
> 
> 
> 
>

[Package ade4 Index]