chronopl {ape}R Documentation

Molecular Dating With Penalized Likelihood

Description

This function estimates the node ages of a tree using semi-parametric method based on penalized likelihood (Sanderson 2002). The branch lengths of the input tree are interpreted as (mean) numbers of substitutions.

Usage

chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE)

Arguments

phy an object of class "phylo".
lambda value of the smoothng parameter.
node.age numeric values specifying the fixed node ages.
node the numbers of the nodes whose ages are given by node.age; "root" is a short-cut the number of the node.
CV whether to perform cross-validation.

Details

The idea of this method is to use a trade-off between a parametric formulation where each branch has its own rate, and a nonparametric term where changes in rates are minimized between contiguous branches. A smoothing parameter (lambda) controls this trade-off. If lambda = 0, then the parametric component dominates and rates vary as much as possible among branches, whereas for increasing values of lambda, the variation are smoother to tend to a clock-like model (same rate for all branches).

lambda must be given. The known ages are given in node.age, and the correponding node numbers in node. These two arguments must obviously be of the same length. By default, an age of 1 is assumed for the root, and the ages of the other nodes are estimated.

The cross-validation used here is different from the one proposed by Sanderson (2002). Here, each tip is dropped successively and the analysis is repeated with the reduced tree: the estimated dates for the remaining nodes are compared with the estimates from the full data. For the ith tip the following is calculated:

SUM[j = 1, ..., n-2] (tj - tj[-i])^2/tj

,

where tj is the estimated date for the jth node with the full phylogeny, tj[-i] is the estimated date for the jth node after removing tip i from the tree, and n is the number of tips.

Value

an object of class "phylo" with branch lengths as estimated by the function. There are two or three further attributes:

ploglik the maximum penalized log-likelihood.
rates the estimated rates for each branch.
D2 the influence of each observation on overall date estimates (if CV = TRUE).

Author(s)

Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr

References

Sanderson, M. J. (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101–109.

See Also

chronogram, ratogram, NPRS.criterion


[Package ape version 1.10-1 Index]