Fit regressions on species abundance or presence/absence across communities and calculate phylogenetic correlations
1 2 3 4  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"))

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 
sppreg 
object from function 
rows 

cex.mag 
value for 
x.label 
x axis labels 
y.label 
y axis labels 
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^2n)/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 cooccurrence once the environmental variables are taken into account). The significance of these correlations can be tested
via permutation with the function phylostruct
.
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 
The function requires the library brglm
to perform logistic regressions
Matthew Helmus mrhelmus@gmail.com
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, 917925
phylostruct
, phylosignal
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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