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These are the facts: I am working with some morphological features. Each trait can have one of the following three states: 0, 1, 2.

State 0 is always independent.

But if there is a trait with state 1, then there must be, in another column of the same row, a state 2 (and vice versa, obviously).

The traits can't be encoded separately because, eg, in the row_01, at the trait_01, the state 1 is ligated to the trait_20 with state 2. But in another row (row_02), the trait_01 with state 1 could be ligated to another trait (trait_33) with state 2. My data behaves like this because I'm working with morphology in... molecules.

So far, I know that the data of an array in phylogeny must be independent, so I am wondering if any of you know of any way to approach this problem (paper, algorithm, your own propose, etc.).

solving conditions:

  • I can't discard the traits with state 1 or 2.

Cheers!

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  • $\begingroup$ I am not sure that I understand. If the traits fully determine each other, why are they encoded separately? It might help to see a sample of the data. If traits were even slightly decomposable one might suggest an ordination method (like PCA) to find independent eigentraits, for example adn.biol.umontreal.ca/~numericalecology/Reprints/…. $\endgroup$
    – Maximilian Press
    Commented Jun 6, 2021 at 23:50
  • $\begingroup$ Since I last looked at this question, the editing appears to have obfuscated it. e.g. My data behaves like this because I'm working with morphology in... molecules. what does it mean for data to be "ligated"? $\endgroup$
    – Maximilian Press
    Commented Jun 9, 2021 at 4:08

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