phylog
.
phylog.extract
returns objects of class phylog
. It extracts sub-trees from a tree.
phylog.permut
returns objects of class phylog
. It creates the different representations compatible with tree topology.print.phylog(x, ...)
phylog.extract(phylog, node, distance = TRUE)
phylog.permut(phylog, list.nodes = NULL, distance = TRUE))
phylog
phylog
:'dist'
. Matrix values $Wdist_{ij}$ correspond to $Ollier, S., Couteron, P. and Chessel, D. (submitted) Orthonormal transforms to detect and describe phylogenetic autocorrelation. Biometrics.
newick2phylog
, plot.phylog
marthans.tre <- NULL
marthans.tre[1] <-"((((1:4,2:4)a:5,(3:7,4:7)b:2)c:2,5:11)d:2,"
marthans.tre[2] <- "((6:5,7:5)e:4,(8:4,9:4)f:5)g:4);"
marthans.phylog <- newick2phylog(marthans.tre)
marthans.phylog
if (require(ape, quietly=TRUE)) {
marthans.phylo <- read.tree(text = marthans.tre)
marthans.phylo
par(mfrow =c (1,2))
plot.phylog(marthans.phylog, cnode = 3, f = 0.8, cle = 3)
plot.phylo(marthans.phylo)
par(mfrow = c(1,1))
}
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