Theory, Examples & Exercises
Borcard et al. (2011) use this data as example dataset; data comes from PhD thesis of Verneaux (1973).
(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.
Doubs river, which runs near France-Switzerland border in the Jura Mountains.
|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]|
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 -