vegtf: Vegetation in Trois-Fontaines

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

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(requireNamespace("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)
  
  if(adegraphicsLoaded()) {
    g1 <- s.value(vegtf$xy, coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = F)
    g2 <- s.value(vegtf$xy, ms.coa1$li[, 1], Sp = vegtf$Spatial, pSp.col = "white", plot = F)
    g3 <- s.label(coa1$c1, plot = F)
    g4 <- s.label(ms.coa1$c1, plot = F)
    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 May 2, 2019, 5:50 p.m.