Re: [R-sig-phylo] MrBayes Branch Lengths in R

[William Gearty]

Resolved; I hadn't taken into account the fact that I needed to scale my
trees by the clock rate.

On Thu, Feb 16, 2017 at 4:32 PM, William Gearty 
wrote:

> Hi all,
>
> I've recently finished a tip-dating analysis (see
> https://www.mail-archive.com/r-sig-phylo@r-project.org/msg04659.html) and
> I'm now trying to import the trees from the posterior (input.nex.run1.t,
> etc.) into R for some comparative analyses.
>
> Using read.nexus, I was able to successfully import the trees, but for
> some reason the branch lengths seem to be off.
> The branch lengths for the consensus tree (from sumt) appear to import
> into R fine (with the root at about 210 Ma), but the posterior trees seem
> to have root ages ranging from 43 to 147.
>
> Am I missing something in my MrBayes nexus file/analysis, which is causing
> the branch lengths to be off in the output file (I was under the impression
> branch lengths are by default printed with the trees)?
> Or is there a different (better) way to import them into R?
>
> Thanks in advance,
> Will
>
> --
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
> people.stanford.edu/wgearty
>



-- 
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
people.stanford.edu/wgearty

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[R-sig-phylo] MrBayes Branch Lengths in R

[William Gearty]

Hi all,

I've recently finished a tip-dating analysis (see
https://www.mail-archive.com/r-sig-phylo@r-project.org/msg04659.html) and
I'm now trying to import the trees from the posterior (input.nex.run1.t,
etc.) into R for some comparative analyses.

Using read.nexus, I was able to successfully import the trees, but for some
reason the branch lengths seem to be off.
The branch lengths for the consensus tree (from sumt) appear to import into
R fine (with the root at about 210 Ma), but the posterior trees seem to
have root ages ranging from 43 to 147.

Am I missing something in my MrBayes nexus file/analysis, which is causing
the branch lengths to be off in the output file (I was under the impression
branch lengths are by default printed with the trees)?
Or is there a different (better) way to import them into R?

Thanks in advance,
Will

-- 
William Gearty
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
people.stanford.edu/wgearty

[[alternative HTML version deleted]]

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