mites: mites dataset
In jSDM: Joint Species Distribution Models
mites R Documentation
mites dataset
Description
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.
Usage
data("mites")
Format
A data frame with 70 observations on the following 42 variables.
Abundance of 35 Oribatid mites morphospecies named :
Brachya vector of integers
PHTHa vector of integers
HPAVa vector of integers
RARDa vector of integers
SSTRa vector of integers
Protopla vector of integers
MEGRa vector of integers
MPROa vector of integers
TVIEa vector of integers
HMINa vector of integers
HMIN2a vector of integers
NPRAa vector of integers
TVELa vector of integers
ONOVa vector of integers
SUCTa vector of integers
LCILa vector of integers
Oribatul1a vector of integers
Ceratoz1a vector of integers
PWILa vector of integers
Galumna1a vector of integers
Steganacarus2a vector of integers
HRUFa vector of integers
Trhypochth1a vector of integers
PPELa vector of integers
NCORa vector of integers
SLATa vector of integers
FSETa vector of integers
Lepidozetesa vector of integers
Eupelopsa vector of integers
Minigalumnaa vector of integers
LRUGa vector of integers
PLAG2a vector of integers
Ceratoz3a vector of integers
Oppia.minusa vector of integers
Trimalaco2a vector of integers
5 covariates collected on the 70 sites and their coordinates :
substratea categorical vector indicating substrate type using a 7-level unordered factor : sph1, sph2, sph3, sph4, litter, peat and inter for interface.
shrubsa categorical vector indicating shrub density using a 3-level ordered factor : None, Few and Many
topoa categorical vector indicating microtopography using a 2-level factor: blanket or hummock
densitya numeric vector indicating the substrate density (g/L)
watera numeric vector indicating the water content of the substrate (g/L)
xa numeric vector indicating first coordinates of sampling sites
ya numeric vector indicating second coordinates of sampling sites
Details
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.
Source
Pierre Legendre
References
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.
Examples
data(mites, package="jSDM")
head(mites)
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mites dataset
Description
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.
Usage
data("mites")Format
A data frame with 70 observations on the following 42 variables.
Abundance of 35 Oribatid mites morphospecies named :
Brachya vector of integers
PHTHa vector of integers
HPAVa vector of integers
RARDa vector of integers
SSTRa vector of integers
Protopla vector of integers
MEGRa vector of integers
MPROa vector of integers
TVIEa vector of integers
HMINa vector of integers
HMIN2a vector of integers
NPRAa vector of integers
TVELa vector of integers
ONOVa vector of integers
SUCTa vector of integers
LCILa vector of integers
Oribatul1a vector of integers
Ceratoz1a vector of integers
PWILa vector of integers
Galumna1a vector of integers
Steganacarus2a vector of integers
HRUFa vector of integers
Trhypochth1a vector of integers
PPELa vector of integers
NCORa vector of integers
SLATa vector of integers
FSETa vector of integers
Lepidozetesa vector of integers
Eupelopsa vector of integers
Minigalumnaa vector of integers
LRUGa vector of integers
PLAG2a vector of integers
Ceratoz3a vector of integers
Oppia.minusa vector of integers
Trimalaco2a vector of integers
5 covariates collected on the 70 sites and their coordinates :
substratea categorical vector indicating substrate type using a 7-level unordered factor :
sph1,sph2,sph3,sph4,litter,peatandinterfor interface.shrubsa categorical vector indicating shrub density using a 3-level ordered factor :
None,FewandManytopoa categorical vector indicating microtopography using a 2-level factor:
blanketorhummockdensitya numeric vector indicating the substrate density (g/L)
watera numeric vector indicating the water content of the substrate (g/L)
xa numeric vector indicating first coordinates of sampling sites
ya numeric vector indicating second coordinates of sampling sites
Details
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.
Source
Pierre Legendre
References
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.
Examples
data(mites, package="jSDM")
head(mites)
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