[Mesquitelist] Likelihood reconstruction of changes: how to generate a table?
david.fitch at nyu.edu
Fri Aug 8 13:56:45 PDT 2008
Dear Mesquite Users/Designers,
For a matrix of discrete binary characters, how does one output a
table that details the likelihood reconstruction of character-state
CHANGES ("losses" and "gains") in each character and each branch?
I see that Mesquite can output a table of the probabilities of HAVING
a particular state at each branch for each character (Analysis >
TraceAllCharacters). And I see that Mesquite can output a table of
changes occurring across a (or many) tree(s) for ONE particular
character at a time (Taxa&Trees > SummarizeStateChangesOverTrees).
However, I cannot figure out how to output a table of CHANGES for
EACH branch for EACH character.
For example, each character could be represented by a row in the table.
Each branch is represented by a pair of columns:
the 1st column with the number of gains,
the 2nd column with the number of losses.
Presumably, the "number of gains" or "number of losses" would not
necessarily be integers, because the probability of a particular
change may not be 1.0 or 0.0 for a particular branch (unless the
decision threshold is applied; e.g. >50% probability for a gain would
be scored as a definite gain for that branch).
Any ideas would be very welcome!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - -
~ David H. A. Fitch ~ \ / / /
~ Associate Professor ~ \/ / /
~ Department of Biology ~ \ / /
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