Table of Contents
Doubs river fish communities
Source of data
Borcard et al. (2011) use this data as example dataset; data comes from PhD thesis of Verneaux (1973).
Description of the dataset
(from Borcard et al. 2011)
In an important doctoral thesis, Verneaux (1973) proposed to use fish species to characterize ecological zones along European rivers and streams. He showed that fish communities were good biological indicators of these water bodies. Starting from the source, Verneaux proposed a typology in four zones, and he named each one after a characteristic species: the trout zone, the grayling zone, the barbel zone and the bream zone. The corresponding ecological conditions, with much variation among rivers, range from relatively pristine, well oxygenated and oligotrophic to eutrophic and oxygen-deprived waters.
Data have been collected at 30 localities along Doubs river. The first matrix contains coded abundances of 27 fish species, the second matrix contains 11 environmental variables related to the hydrology, geomorphology, and chemistry of the river, and the third matrix contains the geographical coordinates (Cartesian, X and Y) of the sites.
Locality
Doubs river, which runs near France-Switzerland border in the Jura Mountains.
Environmental variables
| Code | Description of the variable |
|---|---|
| das | Distance from the source [km] |
| alt | Altitude [m a.s.l.] |
| pen | Slope [per thousand] |
| deb | Mean minimum discharge [m3s-1] |
| pH | pH of water |
| dur | Calcium concentration (hardness) [mgL-1] |
| pho | Phosphate concentration [mgL-1] |
| nit | Nitrate concentration [mgL-1] |
| amn | Ammonium concentration [mgL-1] |
| oxy | Dissolved oxygen [mgL-1] |
| dbo | Biological oxygen demand [mgL-1] |
R script for direct import of data to R
doubs.spe <- read.csv ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/DoubsSpe.csv', row.names = 1) doubs.env <- read.csv ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/DoubsEnv.csv', row.names = 1) doubs.spa <- read.csv ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/DoubsSpa.csv', row.names = 1)
Data are also available from the library ade4 under the name doubs (the variable is a list of three data frames - poi, mil a xy):
# install.packages ('ade4') # uncomment this line if the library is not installed on your computer library (ade4) data (doubs) doubs.spe <- doubs$poi doubs.env <- doubs$mil doubs.spa <- doubs$xy
References
- 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.
- Borcard, D., Gillet, F. & Legendre, P. (2011) Numerical Ecology with R. Springer, UseR! Edition.