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finalproject/Scripts/mcmc_ase_mk.Rev
Line 7 in 6269ce5
Keep time-reversible, but separate STAGE versus CHARACTER versus COLOR transitions, in addition to dependencies.
finalproject/Data/plumage_all.nex
Line 9 in 6269ce5
Explicitly code STAGES as characters, along with
This reintroduces the tripartite plumage patch dependency:
DPM is dependent on dichromatism: P1 | D (i.e., dichromatism)
Inserted stages are dependent on earlier inserted stages: P2 | P1 for example
Predefinitive plumage characters are dependent on plumage stages: P1-Crown | P1
And, to add a color-type dependency:
P1-Crown-Structural | P1-Crown
P1-Crown-Carotenoid | P1-Crown
P1-Crown-Melanin | P1-Crown
This change to character coding will allow the explicit detection of P-STAGE and P-CHARACTER homologies, as well as the separate transition rates for STAGE changes versus CHARACTER changes versus COLOR changes. Need then PARAMO dependency.
finalproject/Scripts/wrangle_plumages.r
Line 31 in 488388a
finalproject/Data/pipridae_trees.nex
Line 8 in 6269ce5
Output from the Jetz BirdTree is a whole distribution of trees. Right now, I am only using one of those trees to clamp in RevBayes for ACE. Is there a way to incorporate this whole distribution of input trees? Does RB accept a "clamp" of multiple trees? Should I collapse all of the trees into a single consensus tree ahead of time?
Line 57 in 6269ce5
Need explicit developmental dependencies in ACE from PARAMO. Integrate .Rev file with dependency chart after plumage patch coding method is complete.
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