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)

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$xy, add.p = TRUE, clab = 1.5)
w <- as.numeric(scalewt(kcponds$tab$N))
s.value(kcponds$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$tab, scan = FALSE, nf = 4)
if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
multi1 <- multispati(pca1, nb2listw(neig2nb(kcponds$neig)),
     scan = FALSE, nfposi = 2, nfnega = 1)
summary(multi1)}
par(mfrow = c(1,1))

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: kcponds
> ### Title: Ponds in a nature reserve
> ### Aliases: kcponds
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(kcponds)
> 
> 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$xy, add.p = TRUE, clab = 1.5)
> w <- as.numeric(scalewt(kcponds$tab$N))
> s.value(kcponds$xy, w, cleg = 2, sub = "Nitrogen concentration",
+      csub = 4, possub = "topright", include = FALSE)
> par(mfrow = c(1,1))
> 
> par(mfrow=c(3,1))
> pca1 <- dudi.pca(kcponds$tab, scan = FALSE, nf = 4)
> if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
+ multi1 <- multispati(pca1, nb2listw(neig2nb(kcponds$neig)),
+      scan = FALSE, nfposi = 2, nfnega = 1)
+ summary(multi1)}
deldir 0.0-12 

     Please note: The process for determining duplicated points
     has changed from that used in version 0.0-9 (and previously).


Multivariate Spatial Analysis
Call: multispati(dudi = pca1, listw = nb2listw(neig2nb(kcponds$neig)), 
    scannf = FALSE, nfposi = 2, nfnega = 1)

Scores from the initial duality diagramm:
         var      cum     ratio      moran
RS1 2.853998 2.853998 0.1902666 0.10811303
RS2 2.238375 5.092373 0.3394915 0.35125502
RS3 1.652132 6.744505 0.4496337 0.05342198
RS4 1.549259 8.293764 0.5529176 0.08290742

Multispati eigenvalues decomposition:
            eig      var      moran
CS1   1.3304839 2.069803  0.6428070
CS2   1.0281673 1.617189  0.6357744
CS15 -0.7079602 1.638742 -0.4320145
> par(mfrow = c(1,1))
> 
> 
> 
> 
> 

[Package ade4 Index]