diversi.time: Analysis of Diversification with Survival Models
Description
This functions fits survival models to a set of branching times, some
of them may be known approximately (censored). Three models are
fitted, Model A assuming constant diversification, Model B assuming
that diversification follows a Weibull law, and Model C assuming that
diversification changes with a breakpoint at time `Tc'. The models are
fitted by maximum likelihood.Usage
diversi.time(x, census = NULL, censoring.codes = c(1, 0), Tc = NULL)
Value
A NULL value is returned, the results are simply printed.Details
The principle of the method is to consider each branching time as an
event: if the branching time is accurately known, then it is a failure
event; if it is approximately knwon then it is a censoring event. An
analogy is thus made between the failure (or hazard) rate estimated by
the survival models and the diversification rate of the lineage. Time
is here considered from present to past. Model B assumes a monotonically changing diversification rate. The
parameter that controls the change of this rate is called beta. If
beta is greater than one, then the diversification rate decreases
through time; if it is lesser than one, the the rate increases through
time. If beta is equal to one, then Model B reduces to Model A.
References
Paradis, E. (1997) Assessing temporal variations in diversification
rates from phylogenies: estimation and hypothesis
testing. Proceedings of the Royal Society of London. Series
B. Biological Sciences, 264, 1141--1147.