Hi Marko.
The following link contains worked examples of several different model
fitting methods that using the "simmap" object class from phytools,
including OUwie:
https://goo.gl/rJRQCn
Here is a very simple example, also with OUwie, using a "multiSimmap"
object:
https://goo.gl/Mbx4hn
I hope this is of some help. Sincerely, Liam
Liam J. Revell, Associate 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 8/11/2017 12:50 PM, Marko Djurakic wrote:
Hello,
I performed stochastic character mapping using make.simmap function from
phytools package (v.0.6-20) with provided prior probabilities of tip
states (3 states). I generated 1000 maps and I want to fit several
evolutionary models to each map in mvMORPH (v.1.0.9) and OUwie (v.1.50)
packages. I aim to estimate the uncertainty due to stochastic mapping.
I was able to do fitting of models using each map in mvMORPH, but I
stuck when I want to do this in OUwie.
OUwie function can use mapped states if the simmap.tree argument is set
to TRUE, but it also requires data frame (argument "data") where I need
to specify three columns: species names, the current selective regime,
and continuous trait.
If I used prior probabilities of states in order to obtain maps, in
turn, how can/should I specify current selective regime required for
"data" argument of OUwie function?
I appreciate any comment or suggestion.
Kind regards,
Marko
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