kcponds: Ponds in a nature reserve

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

Ponds in a nature reserve

Description

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

Usage

data(kcponds)

Format

kponds is a list with the following components:

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

nb

the neighbourhood graph of the 33 sites (an object of class nb)

Spatial

an object of the class SpatialPolygons of sp, containing the map

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.

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$xy, add.p = TRUE, cpoi = 3, clab = 0)
  area.plot(kcponds$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$tab, scan = FALSE, nf = 4)
  if(requireNamespace("spdep", quietly = TRUE) &
    requireNamespace("adespatial", quietly = TRUE)) {
    multi1 <- adespatial::multispati(pca1, spdep::nb2listw(kcponds$nb),
        scannf = FALSE, nfposi = 2, nfnega = 1)
    summary(multi1)
  }
  par(mfrow = c(1, 1))

## End(Not run)

ade4 documentation built on April 3, 2025, 8:22 p.m.