Hi Maria.
It is not correct to choose the model with the highest mean
log-likelihood. make.simmap with Q=mcmc uses Markov Chain Monte Carlo
to sample Q matrices from their Bayesian posterior probabilities (using
priors control parameters of the MCMC, including proposal
distributions,
Hi!
Liam, Tony, Sam, thank you for the answers! They forced me to think on type of
model I've chosen.
I forgot to mention previously that I have used only one input tree. I choose
the model ARD, because it was the best model (among SYM and ER) according to
fitDiscrete (geiger).
Installation
Hi Maria,
In addition to Liam and Sam’s comments you may want to look at some of your
trees individually. It is possible you have conflicting topologies that fit
quite different transition rate matrices. Examining the transition rates from
individual trees will let you determine if they fit one
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
Hi Maria,
If you are running these analyses across a set of trees it maybe how you are
compiling the output, as sometimes the order of the output is dependent on the
root state which can change. It is easy to see if this is the problem by just
sorting the output before you compile it.
Sam
