sppregs {picante}R Documentation

Regressions to Separate Phylogenetic Attraction and Repulsion

Description

Fit regressions on species abundance or presence/absence across communities and calculate phylogenetic correlations

Usage

sppregs(samp, env, tree=NULL, fam="gaussian")
sppregs.plot(sppreg, rows=c(1,3), cex.mag=1, x.label="phylogenetic correlations", 
y.label=c("occurrence correlations w/ env","occurrence correlations wo/ env","change in correlations"))

Arguments

samp community data matrix, species as columns, communities as rows
env environmental data matrix
tree phylo tree object or a phylogenetic covariance matrix
fam with fam = "gaussian" fits with glm; with fam = "binomial" fit logistic regressions with Firth's bias-reduction using brglm
sppreg object from function sppregs
rows rows = c(1,3) plots in a row; rows = c(3,1) in a column
cex.mag value for cex in par
x.label x axis labels
y.label y axis labels

Details

For each species in samp, the function fits regressions of species presence/absence or abundances on the environmental variables supplied in env; and calculates the (n^2-n)/2 pairwise species correlations between the residuals of these fits and pairwise species phylogenetic correlations. The residuals can be thought of as the presence/absence of species across sites/communities after accounting for how species respond to environmental variation across sites. Each set of coefficients can be tested for phylogenetic signal with, for example, the function phylosignal.

The function sppregs.plot produces a set of three plots of the correlations of pairwise species phylogenetic correlations versus: the observed pairwise correlations of species across communities, the residual correlations, and the pairwise differences between (i.e., the change in species co-occurrence once the environmental variables are taken into account). The significance of these correlations can be tested via permutation with the function phylostruct.

Value

family the regression error distribution
residuals the residuals from each species regression
coefficients the estimated coefficients from each species regression
std.errors the standard errors of the coefficients
correlations correlations of pairwise species phylogenetic correlations between: the observed pairwise correlations of species across communities, the residual correlations, and the pairwise differences between the two
cors.pa the observed pairwise correlations of species across communities
cors.resid the residual pairwise correlations of species across communities
cors.phylo the phylogenetic pairwise correlations among species

Note

The function requires the library brglm to perform logistic regressions

Author(s)

Matthew Helmus mrhelmus@gmail.com

References

Helmus M.R., Savage K., Diebel M.W., Maxted J.T. & Ives A.R. (2007) Separating the determinants of phylogenetic community structure. Ecology Letters, 10, 917-925

See Also

phylostruct, phylosignal


[Package picante version 0.6-1 Index]