Dear Erwan,
there are two different functions 'pml' which estimates the likelihood for
the given parameters and returns an object of class 'pml' and 'optim.pml'
which performs optimisation on an object of class 'pml'.
In your case you first to construct an object of class 'pml'
assume you have
Hi everyone,
Phangorn package allows to perform ML trees after having chosen a model.
I've run jmodeltest which has told me that a model GTR+G would be
appropriate for my data.
I would like to enter the different parameters in the pml function in
order to draw a tree.
There's an example
