doubs {ade4}R Documentation

Pair of Ecological Tables

Description

This data set gives environmental variables, fish species and spatial coordinates for 30 sites.

Usage

data(doubs)

Format

doubs is a list with 3 components.

mil
is a data frame with 30 rows (sites) and 11 environmental variables.
poi
is a data frame with 30 rows (sites) and 27 fish species.
xy
is a data frame with 30 rows (sites) and 2 spatial coordinates.

Details

The rows of doubs$mil, doubs$poi and doubs$xy are 30 sites along the Doubs, a French and Switzerland river.

doubs$mil contains the following variables: das - distance to the source (km * 10), alt - altitude (m), pen (log(x + 1) where x is the slope (per mil * 100), deb - minimum average debit (m3/s * 100), pH (* 10), dur - total hardness of water (mg/l of Calcium), pho - phosphates (mg/l * 100), nit - nitrates (mg/l * 100), amm - ammonia nitrogen (mg/l * 100), oxy - dissolved oxygen (mg/l * 10), dbo - biological demand for oxygen (mg/l * 10).

doubs$poi contains the abundance of the following fish species: Cottus gobio (CHA), Salmo trutta fario (TRU), Phoxinus phoxinus (VAI), Nemacheilus barbatulus (LOC), Thymallus thymallus (OMB), Telestes soufia agassizi (BLA), Chondrostoma nasus (HOT), Chondostroma toxostoma (TOX), Leuciscus leuciscus (VAN), Leuciscus cephalus cephalus (CHE), Barbus barbus (BAR), Spirlinus bipunctatus (SPI), Gobio gobio (GOU), Esox lucius (BRO), Perca fluviatilis (PER), Rhodeus amarus (BOU), Lepomis gibbosus (PSO), Scardinius erythrophtalmus (ROT), Cyprinus carpio (CAR), Tinca tinca (TAN), Abramis brama (BCO), Ictalurus melas (PCH), Acerina cernua (GRE), Rutilus rutilus (GAR), Blicca bjoerkna (BBO), Alburnus alburnus (ABL), Anguilla anguilla (ANG).

Source

Verneaux, J. (1973) Cours d'eau de Franche-Comté (Massif du Jura). Recherches écologiques sur le réseau hydrographique du Doubs. Essai de biotypologie. Thèse d'état, Besançon. 1–257.

References

See a French description of fish species at http://pbil.univ-lyon1.fr/R/articles/arti049.pdf.
Chesse, D., Lebreton, J.D. and Yoccoz, N.G. (1987) Propriétés de l'analyse canonique des correspondances. Une illustration en hydrobiologie. Revue de Statistique Appliquée, 35, 4, 55–72.

Examples

data(doubs)
pca1 <- dudi.pca(doubs$mil, scan = FALSE)
pca2 <- dudi.pca(doubs$poi, scale = FALSE, scan = FALSE)
coiner1 <- coinertia(pca1, pca2, scan = FALSE)
par(mfrow = c(3,3))
s.corcircle(coiner1$aX)
s.value(doubs$xy, coiner1$lX[,1])
s.value(doubs$xy, coiner1$lX[,2])
s.arrow(coiner1$c1)
s.match(coiner1$mX, coiner1$mY)
s.corcircle(coiner1$aY)
s.arrow(coiner1$l1)
s.value(doubs$xy, coiner1$lY[,1])
s.value(doubs$xy, coiner1$lY[,2])
par(mfrow = c(1,1))

Worked out examples


> library(ade4)
> ### Name: doubs
> ### Title: Pair of Ecological Tables
> ### Aliases: doubs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(doubs)
> pca1 <- dudi.pca(doubs$mil, scan = FALSE)
> pca2 <- dudi.pca(doubs$poi, scale = FALSE, scan = FALSE)
> coiner1 <- coinertia(pca1, pca2, scan = FALSE)
> par(mfrow = c(3,3))
> s.corcircle(coiner1$aX)
> s.value(doubs$xy, coiner1$lX[,1])
> s.value(doubs$xy, coiner1$lX[,2])
> s.arrow(coiner1$c1)
> s.match(coiner1$mX, coiner1$mY)
> s.corcircle(coiner1$aY)
> s.arrow(coiner1$l1)
> s.value(doubs$xy, coiner1$lY[,1])
> s.value(doubs$xy, coiner1$lY[,2])
> par(mfrow = c(1,1))
> 
> 
> 
> 

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