R: Ponds in a nature reserve

kcponds {ade4} | R Documentation

## Ponds in a nature reserve

### Description

This data set contains informations about 33 ponds in De Maten reserve (Genk, Belgium).

### Usage

    data(kcponds)

### Format

tab

  : a data frame with 15 environmental variables(columns) on 33 ponds(rows)

area

  : an object of class `area`

xy

  : a data frame with the coordinates of ponds

neig

  : an object of class `neig`

### Details

Variables of `kcponds$tab` are the following ones : depth, area, O2 (oxygen concentration), cond (conductivity), pH, Fe (Fe concentration), secchi (Secchi disk depth), N (NNO concentration), TP (total phosphorus concentration), chla (chlorophyll-a concentration), EM (emergent macrophyte cover), FM (floating macrophyte cover), SM (submerged macrophyte cover), denMI (total density of macroinvertebrates), divMI (diversity macroinvertebrates)

### Source

Cottenie, K. (2002) Local and regional processes in a zooplankton metacommunity. PhD, Katholieke Universiteit Leuven, Leuven, Belgium.
http://www.kuleuven.ac.be/bio/eco/phdkarlcottenie.pdf

### Examples

    data(kcponds)
    w <- as.numeric(scalewt(kcponds$tab$N))

    if(adegraphicsLoaded()) {
      if(requireNamespace("sp", quietly = TRUE)) {
        g1 <- s.label(kcponds$xy, Sp = kcponds$Spatial, pSp.col = "white", nb = kcponds$nb,
          plab.cex = 0, paxes.asp = "fill", plot = FALSE)
        g2 <- s.label(kcponds$xy, Sp = kcponds$Spatial, pSp.col = "white", plabels.cex = 0.8,
          paxes.asp = "fill", plot = FALSE)
        g3 <- s.value(kcponds$xy, w, psub.text = "Nitrogen concentration", paxe.asp = "fill",
          plot = FALSE)
        G <- rbindADEg(g1, g2, g3, plot = TRUE)
      }

    } else {
      par(mfrow=c(3, 1))
      area.plot(kcponds$area)
      s.label(kcponds$xy, add.p = TRUE, cpoi = 2, clab = 0)
      s.label(kcponds$xy, add.p = TRUE, cpoi = 3, clab = 0)
      s.label(kcponds$xy, add.p = TRUE, cpoi = 0, clab = 0, neig = kcponds$neig, cneig = 1)
      area.plot(kcponds$area)
      s.label(kcponds$xy, add.p = TRUE, clab = 1.5)
      s.value(kcponds$xy, w, cleg = 2, sub = "Nitrogen concentration", csub = 4,
        possub = "topright", include = FALSE)
      par(mfrow = c(1, 1))
    }

    ## Not run:
      par(mfrow = c(3, 1))
      pca1 <- dudi.pca(kcponds$tab, scan = FALSE, nf = 4)
      if(requireNamespace("maptools", quietly = TRUE) & requireNamespace("spdep", quietly = TRUE)) {
        multi1 <- multispati(pca1, spdep::nb2listw(neig2nb(kcponds$neig)), scannf = FALSE, nfposi = 2,
          nfnega = 1)
        summary(multi1)
      }
      par(mfrow = c(1, 1))

    ## End(Not run)

[Package ade4 version 1.7-8 Index]