R

Oribatid mite

calsalmon April 21, 2014
oribatid R Documentation

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 starting from
http://www.fas.umontreal.ca/biol/casgrain/fr/labo/oribates.html

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/pps/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 (require(deldir, quiet = TRUE)) {
  if (require(spdep, quiet = TRUE)) {
    plot(deldir(ori.xy), add = TRUE)
    s.label(ori.xy, add.p = TRUE,
     neig = nb2neig(knn2nb(knearneigh(as.matrix(ori.xy), 3))),
     clab = 0)
    }
  }

Results

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ade4)

Attaching package: 'ade4'

The following object is masked from 'package:base':

    within

> png(filename="/home/oogasawa/snapshot/RGM3/R_CC/result/ade4/oribatid.Rd_%03d_medium.png", width=480, height=480)
> ### Name: oribatid
> ### Title: Oribatid mite
> ### Aliases: oribatid
> ### Keywords: datasets
> 
> ### ** 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 (require(deldir, quiet = TRUE)) {
+   if (require(spdep, quiet = TRUE)) {
+     plot(deldir(ori.xy), add = TRUE)
+     s.label(ori.xy, add.p = TRUE,
+      neig = nb2neig(knn2nb(knearneigh(as.matrix(ori.xy), 3))),
+      clab = 0)
+     }
+   }
deldir 0.0-22
Loading required package: foreign
Loading required package: grid
Loading required package: lattice

Attaching package: 'lattice'

The following object is masked from 'package:boot':

    melanoma

Checking rgeos availability: TRUE

Attaching package: 'spdep'

The following object is masked from 'package:ade4':

    mstree


     PLEASE NOTE:  The components "delsgs" and "summary" of the 
     object returned by deldir() are now DATA FRAMES rather than 
     matrices (as they were prior to release 0.0-18). 
     See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
     duplicated points has changed from that used in version
     0.0-9 of this package (and previously). See help("deldir").

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>