| ratogram {ape} | R Documentation |
ratogram computes a ratogram from a phylogram by applying the NPRS
(nonparametric rate smoothing) algorithm described in Sanderson (1997).
ratogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)
phy |
A phylogenetic tree (i.e. an object of class "phylo"), where
the branch lengths are measured in substitutions. |
scale |
Age of the root in the chronogram corresponding to the inferred ratogram(default value: 0). |
expo |
Exponent in the objective function (default value: 2) |
minEdgeLength |
Minimum edge length in the phylogram (default value: 1e-06). If any branch lengths are smaller then they will be set to this value. |
Please refer to Sanderson (1997) for mathematical details
chronogram returns an object of class "phylo". The branch lengths of this
tree will be the absolute rates estimated for each branch.
Gangolf Jobb (http://www.treefinder.de) and Korbinian Strimmer (http://www.stat.uni-muenchen.de/~strimmer/)
Sanderson, M. J. (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218–1231.
# get tree
data("landplants.newick") # example tree in NH format
tree.landplants <- read.tree(text = landplants.newick)
# plot tree
tree.landplants
plot(tree.landplants, label.offset = 0.001)
# estimate ratogram
rato.plants <- ratogram(tree.landplants)
# plot
plot(rato.plants, label.offset = 0.001)