Hi Maria.
To make sure this is not an error of the software, I highly recommend
you install the latest version of phytools (or at least the latest
version on CRAN). The current CRAN version is 0.4-31. I know in some
earlier version of phytools there was an issue with make.simmap if your
data had more than two states, but this should be fixed in the current
CRAN version.
Having updated phytools (and if the result persists) you might also
compare your result to one obtained using Q="empirical" (the default).
If you do this then the function will use the single most likelihood
value for the transition matrix. This could tell you if the result you
have found is being influenced by the prior (although the mean of the
prior in make.simmap is 'hyper-parameterized' by the ML value of Q, so
this seems somewhat unlikely).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/27/2015 9:28 AM, Maria Ghazali wrote:
Hi!
I am using phytools 0-3.10. I am trying to do ancestral reconstruction with make.simmap
for 3-state discrete character with Q="mcmc", nsim=1000, and default priors
(alpha=beta=1). In the result I have transition rates, Q-matrix, for each of 1000 trees.
The function proposes mean Q-matrix. But I've looked at the histograms of the
between-state transition rates (i.e. state1 to state2, or state2 to state3, etc.). Some
of the transitions have bimodal distribution - with 2 maximums. Some are unimodal.
Is that wrong? Is that a sign of bad model?
Сould I use medians to present the results? To show which transitions are more
frequent.
Thank you,
Maria
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