avimedi: Fauna Table for Constrained Ordinations

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

Fauna Table for Constrained Ordinations

Description

avimedi is a list containing the information about 302 sites :
frequencies of 51 bird species ; two factors (habitats and Mediterranean origin).

Usage

data(avimedi)

Format

This list contains the following objects:

fau

is a data frame 302 sites - 51 bird species.

plan

is a data frame 302 sites - 2 factors : reg with two levels Provence (Pr, South of France) and Corsica (Co) ; str with six levels describing the vegetation from a very low matorral (1) up to a mature forest of holm oaks (6).

nomesp

is a vector 51 latin names.

Source

Blondel, J., Chessel, D., & Frochot, B. (1988) Bird species impoverishment, niche expansion, and density inflation in mediterranean island habitats. Ecology, 69, 1899–1917.

Examples

## Not run: 
data(avimedi)
coa1 <- dudi.coa(avimedi$fau, scan = FALSE, nf = 3)
bet1 <- bca(coa1, avimedi$plan$str, scan = FALSE)
wit1 <- wca(coa1, avimedi$plan$reg, scan=FALSE)
pcaiv1 <- pcaiv(coa1, avimedi$plan, scan = FALSE)
    
if(adegraphicsLoaded()) {
  g1 <- s.class(coa1$li, avimedi$plan$str:avimedi$plan$reg, 
    psub.text = "Correspondences Analysis", plot = FALSE)
  g2 <- s.class(bet1$ls, avimedi$plan$str, psub.text = "Between Analysis", plot = FALSE)
  g3 <- s.class(wit1$li, avimedi$plan$str, psub.text = "Within Analysis", plot = FALSE)

  g41 <- s.match(pcaiv1$li, pcaiv1$ls, plabels.cex = 0, 
    psub.text = "Canonical Correspondences Analysis", plot = FALSE)
  g42 <- s.class(pcaiv1$li, avimedi$plan$str:avimedi$plan$reg, plot = FALSE)
  g4 <- superpose(g41, g42, plot = FALSE)
  
  G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))

} else {
  par(mfrow = c(2,2))
  s.class(coa1$li,avimedi$plan$str:avimedi$plan$reg,
      sub = "Correspondences Analysis")
  s.class(bet1$ls, avimedi$plan$str,
      sub = "Between Analysis")
  s.class(wit1$li, avimedi$plan$str,
      sub = "Within Analysis")
  s.match(pcaiv1$li, pcaiv1$ls, clab = 0,
      sub = "Canonical Correspondences Analysis")
  s.class(pcaiv1$li, avimedi$plan$str:avimedi$plan$reg, 
      add.plot = TRUE)
  par(mfrow=c(1,1))
}

## End(Not run)

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.