ade4: oribatid – R documentation

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oribatid

Oribatid mite

Description

This data set contains informations about environmental control and spatial structure in ecological communities of Oribatid mites.

Usage

data(oribatid)

Format

oribatid is a list containing the following objects :

fau: : a data frame with 70 rows (sites) and 35 columns (Oribatid species)
envir: : a data frame with 70 rows (sites) and 5 columns (environmental variables)
xy: : a data frame that contains spatial coordinates of the 70 sites

Details

Variables of oribatid$envir are the following ones :
substrate: a factor with seven levels that describes the nature of the substratum
shrubs: a factor with three levels that describes the absence/presence of shrubs
topo: a factor with two levels that describes the microtopography
density: substratum density (g.L^-1)
water: water content of the substratum (g.L^-1)

Source

Data prepared by P. Legendre Pierre.Legendre@umontreal.ca and D. Borcard borcardd@magellan.umontreal.ca

References

Borcard, D., and Legendre, P. (1994) Environmental control and spatial structure in ecological communities: an example using Oribatid mites (Acari Oribatei). Environmental and Ecological Statistics, 1, 37–61.

Borcard, D., Legendre, P., and Drapeau, P. (1992) Partialling out the spatial component of ecological variation. Ecology, 73, 1045–1055.

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps039.pdf (in French).

Examples

data(oribatid)
ori.xy <- oribatid$xy[, c(2, 1)]
names(ori.xy) <- c("x","y")
plot(ori.xy,pch = 20, cex = 2, asp = 1)

if(requireNamespace("deldir", quietly = TRUE) & requireNamespace("spdep", quietly = TRUE)) {
  plot(deldir::deldir(ori.xy), add = TRUE)
  if(adegraphicsLoaded()) {
    s.label(ori.xy, nb = spdep::knn2nb(spdep::knearneigh(as.matrix(ori.xy), 3)), plab.cex = 0)
  } else {
    s.label(ori.xy, add.p = TRUE, clab = 0, 
      neig = nb2neig(spdep::knn2nb(spdep::knearneigh(as.matrix(ori.xy), 3))))
  }
}

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release