vegtf {ade4}R Documentation

Vegetation in Trois-Fontaines

Description

This data set contains abundance values (Braun-Blanquet scale) of 80 plant species for 337 sites. Data have been collected by Sonia Said and Francois Debias.

Usage

data(vegtf)

Format

vegtf is a list containing the following objects :

veg
is a data.frame with the abundance values of 80 species (columns) in 337 sites (rows).
xy
is a data.frame with the spatial coordinates of the sites.
area
is data.frame (area) which define the boundaries of the study site.
nb
is a neighborhood object (class nb defined in package spdep)

Source

Dray, S., Said, S. and Debias, F. (2008) Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation. Journal of vegetation science, 19, 45–56.

Examples

if (require(spdep, quiet=TRUE)){
data(vegtf)
coa1 <- dudi.coa(vegtf$veg,scannf=FALSE)
ms.coa1 <- multispati(coa1,listw=nb2listw(vegtf$nb),nfposi=2,nfnega=0,scannf=FALSE)
summary(ms.coa1)
plot(ms.coa1)
par(mfrow=c(2,2))
s.value(vegtf$xy,coa1$li[,1],area=vegtf$area,include.origin=FALSE)
s.value(vegtf$xy,ms.coa1$li[,1],area=vegtf$area,include.origin=FALSE)
s.label(coa1$c1)
s.label(ms.coa1$c1)
}

Worked out examples


> library(ade4)
> ### Name: vegtf
> ### Title: Vegetation in Trois-Fontaines
> ### Aliases: vegtf
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require(spdep, quiet=TRUE)){
+ data(vegtf)
+ coa1 <- dudi.coa(vegtf$veg,scannf=FALSE)
+ ms.coa1 <- multispati(coa1,listw=nb2listw(vegtf$nb),nfposi=2,nfnega=0,scannf=FALSE)
+ summary(ms.coa1)
+ plot(ms.coa1)
+ par(mfrow=c(2,2))
+ s.value(vegtf$xy,coa1$li[,1],area=vegtf$area,include.origin=FALSE)
+ s.value(vegtf$xy,ms.coa1$li[,1],area=vegtf$area,include.origin=FALSE)
+ s.label(coa1$c1)
+ s.label(ms.coa1$c1)
+ }
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 = coa1, listw = nb2listw(vegtf$nb), scannf = FALSE, 
    nfposi = 2, nfnega = 0)

Scores from the initial duality diagramm:
          var       cum      ratio      moran
RS1 0.5237982 0.5237982 0.04018794 0.08653081
RS2 0.4852328 1.0090310 0.07741699 0.08012944

Multispati eigenvalues decomposition:
          eig       var    moran
CS1 0.1689640 0.4047914 0.417410
CS2 0.1306298 0.3131971 0.417085
> 
> 
> 
> 

[Package ade4 Index]