Dear Felipe.
My suggestion would be to code the polymorphic condition as a third
state -- so (if your trait is binary) you have three different character
states: 0, 0+1, and 1.
Then you would enter your data as follows:
states: [0, 0+1, 1]
definitely in state zero: [1.0, 0.0, 0.0]
Hi everyone!
I am setting up a presence/absence matrix for running stochastic mapping
through the make.simmap function of phytools, but containing both taxa with
polymorphic character state and with unknown data there. I know it is
possible to represent missing data as probabilities instead of
