mites.Rd
This example data set is composed of 70 cores of mostly Sphagnum mosses collected on the territory of the Station de biologie des Laurentides of University of Montreal, Quebec, Canada in June 1989.
The whole sampling area was 2.5 m x 10 m in size and thirty-five taxa were recognized as species, though many were not given a species name, owing to the incomplete stage of systematic knowledge of the North American Oribatid fauna.
The data set comprises the abundances of 35 morphospecies, 5 substrate and micritopographic variables, and the x-y Cartesian coordinates of the 70 sampling sites.
See Borcard et al. (1992, 1994) for details.
data("mites")
Oribatid mites (Acari: Oribatida) are a very diversified group of small (0.2-1.2 mm) soil-dwelling, mostly microphytophagous and detritivorous arthropods. A well aerated soil or a complex substrate like Sphagnum mosses present in bogs and wet forests can harbour up to several hundred thousand individuals per square metre.
Local assemblages are sometimes composed of over a hundred species, including many rare ones. This diversity makes oribatid mites an interesting target group to study community-environment relationships at very local scales.
A data frame with 70 observations on the following 42 variables.
Brachy
a vector of integers
PHTH
a vector of integers
HPAV
a vector of integers
RARD
a vector of integers
SSTR
a vector of integers
Protopl
a vector of integers
MEGR
a vector of integers
MPRO
a vector of integers
TVIE
a vector of integers
HMIN
a vector of integers
HMIN2
a vector of integers
NPRA
a vector of integers
TVEL
a vector of integers
ONOV
a vector of integers
SUCT
a vector of integers
LCIL
a vector of integers
Oribatul1
a vector of integers
Ceratoz1
a vector of integers
PWIL
a vector of integers
Galumna1
a vector of integers
Steganacarus2
a vector of integers
HRUF
a vector of integers
Trhypochth1
a vector of integers
PPEL
a vector of integers
NCOR
a vector of integers
SLAT
a vector of integers
FSET
a vector of integers
Lepidozetes
a vector of integers
Eupelops
a vector of integers
Minigalumna
a vector of integers
LRUG
a vector of integers
PLAG2
a vector of integers
Ceratoz3
a vector of integers
Oppia.minus
a vector of integers
Trimalaco2
a vector of integers
substrate
a categorical vector indicating substrate type using a 7-level unordered factor : sph1
, sph2
, sph3
, sph4
, litter
, peat
and inter
for interface.
shrubs
a categorical vector indicating shrub density using a 3-level ordered factor : None
, Few
and Many
topo
a categorical vector indicating microtopography using a 2-level factor: blanket
or hummock
density
a numeric vector indicating the substrate density (g/L)
water
a numeric vector indicating the water content of the substrate (g/L)
x
a numeric vector indicating first coordinates of sampling sites
y
a numeric vector indicating second coordinates of sampling sites
Pierre Legendre
Borcard, D.; Legendre, P. and Drapeau, P. (1992) Partialling out the spatial component of ecological variation. Ecology 73: 1045-1055.
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. and Legendre, P. (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecological Modelling 153: 51-68.
data(mites, package="jSDM")
head(mites)
#> Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA TVEL ONOV
#> 1 17 5 5 3 2 1 4 2 2 1 4 1 17 4
#> 2 2 7 16 0 6 0 4 2 0 0 1 3 21 27
#> 3 4 3 1 1 2 0 3 0 0 0 6 3 20 17
#> 4 23 7 10 2 2 0 4 0 1 2 10 0 18 47
#> 5 5 8 13 9 0 13 0 0 0 3 14 3 32 43
#> 6 19 7 5 9 3 2 3 0 0 20 16 2 13 38
#> SUCT LCIL Oribatul1 Ceratoz1 PWIL Galumna1 Steganacarus2 HRUF Trhypochth1
#> 1 9 50 3 1 1 8 0 0 0
#> 2 12 138 6 0 1 3 9 1 1
#> 3 10 89 3 0 2 1 8 0 3
#> 4 17 108 10 1 0 1 2 1 2
#> 5 27 5 1 0 5 2 1 0 1
#> 6 39 3 5 0 1 1 8 0 4
#> PPEL NCOR SLAT FSET Lepidozetes Eupelops Minigalumna LRUG PLAG2 Ceratoz3
#> 1 0 0 0 0 0 0 0 0 0 0
#> 2 1 2 2 2 1 0 0 0 0 0
#> 3 0 2 0 8 0 0 0 0 0 0
#> 4 1 3 2 12 0 0 0 0 0 0
#> 5 0 0 0 12 2 0 0 0 0 0
#> 6 0 1 0 10 0 0 0 0 0 0
#> Oppia.minus Trimalaco2 substrate shrubs topo density water x y
#> 1 0 0 sph1 few hummock 39.179 350.148 0.2 0.1
#> 2 0 0 litter few hummock 54.989 434.815 1.0 0.1
#> 3 0 0 inter few hummock 46.069 371.720 1.2 0.3
#> 4 0 0 sph1 few hummock 48.187 360.501 1.4 0.5
#> 5 0 0 sph1 few hummock 23.551 204.126 2.4 0.7
#> 6 0 0 sph1 few hummock 57.318 311.551 1.8 0.9