Hi Eugen, maybe this is because you don't say how to measure "co-occurence".
An idea with the data from picante: library(picante) data(phylocom) phy <- phylocom$phylo comm <- phylocom$sample # a kind of phylogenetic distance between species (all species of the tree) phd <- cophenetic(phy) #the same but selecting only species occuring in your communities phd2 <- phd[dimnames(comm)[[2]], dimnames(comm)[[2]]] # a kind of coocurence measure (I wouldn't trust this too much ...) coo <- dist(t(comm)) # the plot plot(coo, as.dist(phd2), xlab="co-occurence", ylab="phylogenetic distance") Cheers, Marcelino At 12:51 18/07/2011, Eugen wrote: >HI@all, > >guess I made something wrong, cause my question didn't show up. Anyway, >I was looking for a way to plot co-occurrence vs. phylogenetic distance >in R. I'm working with picante but there seems to be no such function in >the package. Anyone an idea? > >greets > >Eugen >-- >Eugen Egorov >PhD Student >Department of Ecology - Animal Ecology >Faculty of Biology >Philipps-Universität Marburg >Karl-von-Frisch-Str. 8 >35032 Marburg >Germany > >mail: [email protected] >phone: +49 6421 28 23490 > >_______________________________________________ >R-sig-phylo mailing list >[email protected] >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ____________________________________ Marcelino de la Cruz Rot Depto. Biologia Vegetal EUIT Agricola Universidad Politecnica de Madrid tel: 34 + 913365435 ____________________________________ [[alternative HTML version deleted]]
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