hspider: Hunting Spider Data

Description

Abundance of hunting spiders in a Dutch dune area.

Usage

data(hspider)

Arguments

Details

The data, which originally came from Van der Aart and Smeek-Enserink (1975) consists of abundances (numbers trapped over a 60 week period) and 6 environmental variables. There were 28 sites.

This data set has been often used to illustrate ordination, e.g., using canonical correspondence analysis (CCA). In the example below, the data is used for constrained quadratic ordination (CQO; formerly called canonical Gaussian ordination or CGO), a numerically intensive method that has many superior qualities. See cqo for details.

References

Van der Aart, P. J. M. and Smeek-Enserink, N. (1975) Correlations between distributions of hunting spiders (Lycosidae, Ctenidae) and environmental characteristics in a dune area. Netherlands Journal of Zoology, 25, 1--45.

Examples

Run this code

str(hspider)

# Fit a rank-1 Poisson CQO
set.seed(111)  # This leads to the global solution
hspider[,1:6]=scale(hspider[,1:6]) # Standardize the environmental variables
# vvv p1 = cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute, Arctperi, Auloalbi,
# vvv                Pardlugu, Pardmont, Pardnigr, Pardpull, Trocterr, Zoraspin) ~
# vvv          WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
# vvv          fam = poissonff, data = hspider, Crow1posit=FALSE)
# vvv nos = ncol(p1@y)
# vvv lvplot(p1, y=TRUE, lcol=1:nos, pch=1:nos, pcol=1:nos) 
# vvv Coef(p1)
# vvv summary(p1)



# Fit a rank-1 binomial CAO
hsbin = hspider   # Binary species data
hsbin[,-(1:6)] = as.numeric(hsbin[,-(1:6)] > 0)
set.seed(123)
ahsb1 = cao(cbind(Alopcune,Arctlute,Auloalbi,Zoraspin) ~
            WaterCon + ReflLux, family = binomialff(mv=TRUE),
            df1.nl = 2.2, Bestof=3, data = hsbin)
par(mfrow=2:1, las=1)
lvplot(ahsb1, type="predictors", llwd=2, ylab="logit p", lcol=1:9)
persp(ahsb1, rug=TRUE, col=1:10, lwd=2)
coef(ahsb1)