This repository contains vignette and scripts for setting up and running Embedded Dependency (ED) models for phylogenetic inference with inapplicable morphological data (Tarasov 2022).
- Here is a vignette for setting up ED models and rate matrices to run in RevaBayes or other R packages.
- Below are the scripts for reproducing analyses from Tarasov (2022).
The scripts used in Tarasov (2022)
You can download the entire repository by clicking on the green Code button and then selecting Download ZIP in the upper right corner. Or by using this command from within terminal:
git clone https://github.com/sergeitarasov/MorphoModels-
1_ED_model_performance The scripts for "1. ED models and SMMs: fixed data".
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- RevBayes scripts for running tree inference with the ED models and calculating marginal likelihood under fixed data.
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2_EDvsHMM The scripts for "1. ED models and SMMs: fixed data".
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- RevBayes scripts for tree inference (and marginal likelihood calculation) with expanded ED models and SMM under fixed data.
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3_ED_TailColor_problem The scripts for "3. ED and Tail Color Problem".
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- RevBayes scripts to test the resolution of LTC in the tail color problem under fixed data.
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4a_EDvsHMM_topology The scripts for "2. ED models vs. SMMs: simulated data".
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- R scripts (in RB_run_1/4a_R) to simulate trees and characters under the ED6 model.
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- RevBayes scripts to perform tree inferences under the ED6, ED3, and two SMMs.
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- R scripts (in RB_run_1/4a_R) to calculate boostrapped p-values.
Tarasov, S., 2023. New phylogenetic Markov models for inapplicable morphological characters. Systematic Biology, 72(3), pp.681-693. https://academic.oup.com/sysbio/article/72/3/681/7036827.