chronopl(phy, lambda, age.min = 1, age.max = NULL, node = "root", S = 1, tol = 1e-8, CV = FALSE, eval.max = 500, iter.max = 500, ...)"phylo".age.max = NULL) or the youngest bound of the nodes known to
be within an interval.age.min; "root" is a short-cut for the root.nlminb."phylo" with branch lengths as estimated by
the function. There are three or four further attributes: lambda must be given. The known ages are given in
age.min, 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.
If age.max = NULL (the default), it is assumed that
age.min gives exactly known ages. Otherwise, age.max and
age.min must be of the same length and give the intervals for
each node. Some node may be known exactly while the others are
known within some bounds: the values will be identical in both
arguments for the former (e.g., age.min = c(10, 5), age.max =
c(10, 6), node = c(15, 18) means that the age of node 15 is 10
units of time, and the age of node 18 is between 5 and 6).
If two nodes are linked (i.e., one is the ancestor of the other) and
have the same values of age.min and age.max (say, 10 and
15) this will result in an error because the medians of these values
are used as initial times (here 12.5) giving initial branch length(s)
equal to zero. The easiest way to solve this is to change slightly the
given values, for instance use age.max = 14.9 for the youngest
node, or age.max = 15.1 for the oldest one (or similarly for
age.min).
The input tree may have multichotomies. If some internal branches are of zero-length, they are collapsed (with a warning), and the returned tree will have less nodes than the input one. The presence of zero-lengthed terminal branches of results in an error since it makes little sense to have zero-rate branches.
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 $i$th tip the following is calculated:
$$\sum_{j=1}^{n-2}{\frac{(t_j - t_j^{-i})^2}{t_j}}$$,
where $tj$ is the estimated date for the $j$th node with the full phylogeny, $tj[-i]$ is the estimated date for the $j$th node after removing tip $i$ from the tree, and $n$ is the number of tips.
The present version uses the nlminb to optimise
the penalized likelihood function: see its help page for details on
parameters controlling the optimisation procedure.
chronos, chronoMPL