phylo_corr: Phylogenetic correction of traits
In phytomosaic/foggy: Species and Trait Responses to Fog Gradients

Description Usage Arguments Details Value References See Also Examples

Remove potential phylogenetic signal from a set of continuous or discrete traits.

1	phylo_corr(phy, tra, ...)

`phy`	phylogenetic tree of class `'phylo'`
`tra`	matrix or data.frame, rows=species and cols=traits
`...`	additional arguments (currently ignored)

Removes phylogenetic signal from trait values, by applying correction factors obtained from Cholesky decomposition of the phylogenetic variance-covariance matrix (Butler et al. 2000). Current implementation follows Eklöf and Stouffer (2016) in permitting both continuous and categorical traits.

Data frame of same dimensions as tra, but with phylogenetically-corrected values.

Butler, M.A., T.W. Schoener, and J.B. Losos. 2000. The relationship between sexual size dimorphism and habitat use in Greater Antillean Anolis lizards. Evolution 54:259-272.
Eklöf, A., and D.B. Stouffer. 2016. The phylogenetic component of food web structure and intervality. Theoretical Ecology 9:107–115.

Code adapted from: https://github.com/stoufferlab/phyloint/

data(veg) # load('./data/veg.rda', verbose=T)
phy <- veg$phy
tra <- veg$tra
ptra <- phylo_corr(phy, tra)
ecole::set_par(8)
for(i in 1:8){
     plot(tra[,i], ptra[,i], pch=16, cex=0.7, col='#00000050',
     xlab=dimnames(tra)[[2]][i], ylab=dimnames(ptra)[[2]][i])
}