chronogram {ape} | R Documentation |
chronogram
computes a chronogram from a phylogram by applying the NPRS
(nonparametric rate smoothing) algorithm described in Sanderson (1997).
chronogram(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 inferred chronogram (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 clock-like and scaled so that the root node has age 1 (or the value
set by the option scale
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.
library(ape) # 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 chronogram chrono.plants <- chronogram(tree.landplants) # plot and write to file plot(chrono.plants, label.offset = 0.001) write.tree(chrono.plants, file = "chronogram.phy") # value of NPRS function for our estimated chronogram NPRS.criterion(tree.landplants, chrono.plants)