chronos
replaces chronopl
but with a different interface
and some extensions (see References). The known dates (argument calibration
) must be given in a data
frame with the following column names: node, age.min, age.max, and
soft.bounds (the last one is yet unused). For each row, these are,
respectively: the number of the node in the ``phylo'' coding standard,
the minimum age for this node, the maximum age, and a logical value
specifying whether the bounds are soft. If age.min = age.max, this
means that the age is exactly known. This data frame can be built with
makeChronosCalib
which returns by default a data frame with a
single row giving age = 1 for the root. The data frame can be built
interactively by clicking on the plotted tree.
The argument control
allows one to change some parameters of
the optimisation procedure. This must be a list with names. The
available options with their default values are:
{tolerance for the estimation of the substitution
rates.}
- iter.max = 1e4:
{the maximum number of iterations at each
optimization step.}
- eval.max = 1e4:
{the maximum number of function evaluations at
each optimization step.}
- nb.rate.cat = 10:
{the number of rate categories if model
= "discrete"
(set this parameter to 1 to fit a strict clock
model).}
- dual.iter.max = 20:
{the maximum number of alternative
iterations between rates and dates.}