R: Fauna Table for Constrained Ordinations

avimedi {ade4} | R Documentation

## 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)

[Package ade4 version 1.7-8 Index]