That's definitely helpful, Joseph, but I'll need to extend the tips to
varying amounts.

Basically, I performed a tip-dating analysis using constraints based on the
FADs of a bunch of fossils.
However, now some of the analyses I want to perform require that the tips
extend to the species' extinctions, so I need to extend them to the LADs
(or farther, I suppose).
How would I, given a vector of LAD ages for the tips, extend the tips to
those ages?

On Wed, Jul 26, 2017 at 8:50 AM, Joseph W. Brown <josep...@umich.edu> wrote:

> If you want to just extend all tips by a constant amount you can do this:
>
> # extend terminal edges by arbitrary amount (here: 13)
> idx <- which(phy$edge[,2] < (phy$Nnode + 1));
> phy$edge.length[idx] <- phy$edge.length[idx] + 13;
>
> HTH.
> Joseph.
> ________________________________________
> Joseph W. Brown
> Post-doctoral Researcher, Smith Laboratory
> University of Michigan
> Department of Ecology & Evolutionary Biology
> Room 2071, Kraus Natural Sciences Building
> Ann Arbor MI 48109-1079
> josep...@umich.edu
>
>
>
> On 26 Jul, 2017, at 11:39, David Bapst <dwba...@gmail.com> wrote:
>
> Not sure what you mean by extending tips, Will. Could you describe a
> small example?
> -Dave
>
> On Fri, Jul 21, 2017 at 5:15 PM, William Gearty <wgea...@stanford.edu>
> wrote:
>
> Hi all,
>
> Before I go ahead and wrote a whole script, I was wondering if there is a
> function or script out there for extending tips (or setting the ages of
> tips) given a list of taxa and ages?
> I haven't found anything, but perhaps I'm searching the wrong phrase(s).
>
> Thanks,
> Will
>
> --
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
> williamgearty.com
>
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>
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>
>
>
> --
> David W. Bapst, PhD
> https://github.com/dwbapst/paleotree
>
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>
>


-- 
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
williamgearty.com

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