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 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)) {
      data(vegtf)
      coa1 <- dudi.coa(vegtf$veg, scannf = FALSE)
      ms.coa1 <- multispati(coa1, listw = spdep::nb2listw(vegtf$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)
      }
    }

[Package ade4 version 1.7-13 Index]