eSpider: Hunting spider data

In JenniNiku/gllvm: Generalized Linear Latent Variable Models

Hunting spider data

Description

Extended dataset of counts of hunting spiders in a dune area in the Netherlands, measured at 100 pitfall traps.

Usage

data(eSpider)

Format

abund

A data frame with abundances of 12 hunting spider species measured at 100 sites.

X

A matrix of 26 predictor variables at 28 of the 100 sites.

nonNA

An vector of indices indicating at which sites the predictor variables were measured.

Details

Counts of hunting spiders in a dune area in the Netherlands, measured with 100 different pitfall traps. This dataset was published with permission from the CANOCO FORTRAN package (version 4 or higher) example datasets.

Species names have been abbreviated, corresponding to: Alopacce = Alopecosa accentuata, Alopcune = Alopecosa cuneata, Alopfabr = Alopecosa fabrilis, Arctlute = Arctosa lutetiana, Arctperi = Arctosa perita, Auloalbi = Aulonia albimana, Pardlugu = Pardosa lugubris, Pardmont = Pardosa monticola, Pardnigr = Pardosa nigriceps, Pardpull = Pardosa pullata, Trocterr = Trochosa terricola, Zoraspin = Zora spinimana.

Environmental measurements were taken at 28 of the 100 pitfall traps measuring soil properties(Water content: "conWate", Humus content: "conHumu", Acidity (pH-KCl)), vegetation ("BareSand": percentage bare sand, "FallTwig": cover on the ground by leaves and twigs, "CovMoss": cover by mosses and lichens, "CovHerb": cover by the herb and grass layer (including maximum height, minimum height, "CovCala": cover by Calamagrostis epigejos, cover by Carex arenaria, "CovFest": cover by Festuca ovina, "CovCory": cover by Corynephorus canescens, "CovUrti": cover by Urtica dioica, "CovMoeh": cover by Moehringia trinervia), "CovShru": cover by the shrub layer (minimum and maximum height, and "CovLigu": cover by Ligustrum vulgare), "CovTree": cover by the tree layer (including maximum height, cover by Populus tremula or Crataegus monogyna)), and light properties ("LuxGrey": lux at equal grey sky, "LuxSun": lux at cloudless sky, "LuxRef": lux by reflection of the soil surface)

The original publication of Canonical Correspondence Analysis used standardized versions of the log and log1p transformed predictors "ConWate", "BareSand", "FallTwig", "CovMoss", "CovHerb", "LuxRef".

References

ter Braak, C.J.F. and Smilauer, P. (1998). CANOCO reference manual and user's guide to CANOCO for Windows: software for canonical community ordination (version 4). Microcomputer Power, New York, New York, USA. ter Braak, C.J.F. (1986). Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology, 67(5), 1167-1179. Van der Aart, P. J. M. and Smeenk-Enserink, N. (1975). Correlations between distributions of hunting spiders (Lycosidae, Ctenidae) and environmental characteristics in a dune area. Netherlands Journal of Zoology, 25(1), 1-45.

Examples

data(eSpider)
Y <- eSpider$abund[eSpider$nonNA, ]
X <- eSpider$X[eSpider$nonNA, ]
model <- gllvm(y = Y, X = X, 
    lv.formula = ~log(ConWate) + log1p(BareSand) + log1p(FallTwig) + 
    log1p(CovMoss) + log1p(CovHerb) + log(LuxRef),
    num.RR = 2, 
    family = "poisson")

JenniNiku/gllvm documentation built on April 22, 2024, 11:41 p.m.