vegtf: Vegetation in Trois-Fontaines

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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 with the following components:

veg

a data.frame with the abundance values of 80 species (columns) in 337 sites (rows)

xy

a data.frame with the spatial coordinates of the sites

area

a data.frame (area) which define the boundaries of the study site

sp.names

a vector containing the species latin names

nb

a neighborhood object (class nb defined in package spdep)

Spatial

an object of the class SpatialPolygons of sp, containing the map

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(requireNamespace("spdep", quietly = TRUE) & requireNamespace("adespatial", quietly = TRUE)) {
  data(vegtf)
  coa1 <- dudi.coa(vegtf$veg, scannf = FALSE)
  ms.coa1 <- adespatial::multispati(coa1, listw = spdep::nb2listw(vegtf$nb), nfposi = 2, 
    nfnega = 0, scannf = FALSE)
  summary(ms.coa1)
  plot(ms.coa1)
  
  if(adegraphicsLoaded()) {
    g1 <- s.value(vegtf$xy, coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = FALSE)
    g2 <- s.value(vegtf$xy, ms.coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = FALSE)
    g3 <- s.label(coa1$c1, plot = FALSE)
    g4 <- s.label(ms.coa1$c1, plot = FALSE)
    G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
  } else {
    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)
  }
}

ade4 documentation built on April 3, 2025, 8:22 p.m.