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 presence and
absence, but I do not know how to distinguish missing data from
polymorphic character codes for the analyses.
So, would this following codification of missing data and polymorphic
state be correct ?
*Taxon_A,*1,0,0 (character absent)
*Taxon_B*,0,1,0 (character present)
*Taxon_C*,0.5,0.5,0.0 (polymorphic character)
*Taxon_D*,0.33,0.33,0.33 (missing data)
Thank you very much in advance!
Felipe Rossetto
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