Hi Dave-
> Are there any birth-death tree functions which condition on the total
> number of tips (extinct and extant) on a tree rather than the number
> of surviving tips?
You can recode the birthdeath.tree function from Geiger to do this if you want.
The total number of species in the tree (living plus extinct) is equal to
nrow(edge)/2, where "edge" is the edge matrix. Find the repeat statement and
replace the line:
if (taxa.stop)
if (sum(alive) >= taxa.stop)
break
with the following:
if (taxa.stop)
if ((nrow(edge)/2) >= taxa.stop)
break;
The new birthdeath.tree function should stop when taxa.stop lineages have been
born (regardless of whether they've subsequently gone extinct).
> I was wondering if it was known what
> the expected probability distribution of branch lengths for a
> fully-sampled phylogeny (includes all extinct lineages) is?
If you have a perfectly sampled tree, branches should be exponentially
distributed with rate (lambda + mu). Events occur in the birth-death process
with rate (lambda + mu), and the probability that a given event will be
speciation is lambda/(lambda + mu).
~Dan
> I've been
> trying to figure out, if for a fully extinct tree with homogenous
> rates, whether we would expect the branch lengths of internal
> branches to follow an exponential distribution based on the birth
> parameter (and extinct terminal edges following an exponential
> distribution based on the death parameter) or if the branch lengths
> are a function of both parameters. Perhaps I'm not using the right
> keywords, but my literature searches haven't found the information I'm
> looking for.
>
> Thanks,
> -Dave
>
> --
> David Bapst
> Dept of Geophysical Sciences
> University of Chicago
> 5734 S. Ellis
> Chicago, IL 60637
> http://home.uchicago.edu/~dwbapst/
>
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