1.5.1 The Doubs Fish Data
In an important doctoral thesis, Verneaux (1973; see also Verneaux et al. 2003)
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 river source, Verneaux proposed a typology in
four zones, and he named each one after a characteristic species: the trout zone (from
the brown trout Salmo trutta fario), the grayling zone (from Thymallus thymallus),
the barbel zone (from Barbus barbus) and the bream zone (from the common bream
Abramis brama). The two upper zones are considered as the “Salmonid region” and
the two lowermost ones form the “Cyprinid region”. The corresponding ecological
conditions, with much variation among rivers, range from relatively pristine, well
oxygenated and oligotrophic to eutrophic and oxygen-deprived waters.
The Doubs data set that is used in the present book (Doubs.RData) consists of
five data frames, three of them containing a portion of the data used by Verneaux for
his studies. These data have been collected at 30 sites along the Doubs River, which
runs near the France-Switzerland border in the Jura Mountains. 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
in km) of the sites. The Cartesian coordinates have been obtained as follows. One of
us (FG) returned to Verneaux’s thesis to obtain more accurate positions of the
sampling sites than available in existing databases. These new locations were
coded in GPS angular coordinates (WGS84), and transformed into Cartesian coordinates by using function geoXY() of package SoDA in R. Earlier versions of these
data have already served as test cases in the development of numerical techniques
(Chessel et al. 1987). Two additional data frames are provided in the present book’s
material: latlong contains the latitudes and longitudes of the sampling sites, and
fishtraits contains four quantitative variables and six binary variables describing
the diet. Values are taken from various sources, mainly fishbase.org (Froese and
Pauly 2017), checked and adapted to the regional context by François Degiorgi.
1
Working with the original environmental data available in Verneaux’s thesis, one
of us (FG) made some corrections to the data available in R and restored the
variables to their original units, which are presented in Table 1.1.
Since the fish species of this data set have well-defined ecological requirements
that have been often exploited in ecological and applied environmental studies, it is
useful to provide their full Latin and English names. This is done here in Table 1.2.
1 Many thanks to Dr. Degiorgi for this precious work.
1.5 The Data Sets
5
In an important doctoral thesis, Verneaux (1973; see also Verneaux et al. 2003)
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 river source, Verneaux proposed a typology in
four zones, and he named each one after a characteristic species: the trout zone (from
the brown trout Salmo trutta fario), the grayling zone (from Thymallus thymallus),
the barbel zone (from Barbus barbus) and the bream zone (from the common bream
Abramis brama). The two upper zones are considered as the “Salmonid region” and
the two lowermost ones form the “Cyprinid region”. The corresponding ecological
conditions, with much variation among rivers, range from relatively pristine, well
oxygenated and oligotrophic to eutrophic and oxygen-deprived waters.
The Doubs data set that is used in the present book (Doubs.RData) consists of
five data frames, three of them containing a portion of the data used by Verneaux for
his studies. These data have been collected at 30 sites along the Doubs River, which
runs near the France-Switzerland border in the Jura Mountains. 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
in km) of the sites. The Cartesian coordinates have been obtained as follows. One of
us (FG) returned to Verneaux’s thesis to obtain more accurate positions of the
sampling sites than available in existing databases. These new locations were
coded in GPS angular coordinates (WGS84), and transformed into Cartesian coordinates by using function geoXY() of package SoDA in R. Earlier versions of these
data have already served as test cases in the development of numerical techniques
(Chessel et al. 1987). Two additional data frames are provided in the present book’s
material: latlong contains the latitudes and longitudes of the sampling sites, and
fishtraits contains four quantitative variables and six binary variables describing
the diet. Values are taken from various sources, mainly fishbase.org (Froese and
Pauly 2017), checked and adapted to the regional context by François Degiorgi.
1
Working with the original environmental data available in Verneaux’s thesis, one
of us (FG) made some corrections to the data available in R and restored the
variables to their original units, which are presented in Table 1.1.
Since the fish species of this data set have well-defined ecological requirements
that have been often exploited in ecological and applied environmental studies, it is
useful to provide their full Latin and English names. This is done here in Table 1.2.
1 Many thanks to Dr. Degiorgi for this precious work.
1.5 The Data Sets
5