https://github.com/sergeitarasov/morphomodels
Embedded Dependency (ED) models for inapplicable characters
https://github.com/sergeitarasov/morphomodels
anatomy bayesian ed-models inapplicable-characters likelihood markov morphology phylogenetics revbayes
Last synced: 12 days ago
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Embedded Dependency (ED) models for inapplicable characters
- Host: GitHub
- URL: https://github.com/sergeitarasov/morphomodels
- Owner: sergeitarasov
- License: cc0-1.0
- Created: 2021-04-26T16:49:43.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2024-02-26T07:59:59.000Z (over 2 years ago)
- Last Synced: 2024-02-26T09:24:08.759Z (over 2 years ago)
- Topics: anatomy, bayesian, ed-models, inapplicable-characters, likelihood, markov, morphology, phylogenetics, revbayes
- Language: R
- Homepage:
- Size: 13.4 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Embedded Dependency (ED) models for inapplicable morphological characters
# Content
This repository contains [vignette](https://github.com/sergeitarasov/MorphoModels/wiki/Constructing-rate-matrices-for-ED-models) and **scripts** for setting up and running Embedded Dependency (ED) models for phylogenetic inference with inapplicable morphological data [(Tarasov 2022)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3).
* [Here is a vignette](https://github.com/sergeitarasov/MorphoModels/wiki/Constructing-rate-matrices-for-ED-models) 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)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3).
## The scripts used in [Tarasov (2022)](https://www.biorxiv.org/content/10.1101/2021.04.26.441495v3)
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:
``` bash
git clone https://github.com/sergeitarasov/MorphoModels
```
- **1_ED_model_performance** The scripts for "1. ED models and SMMs: fixed data".
- - RevBayes scripts for running tree inference with the ED models and calculating marginal likelihood under fixed data.
- **2_EDvsHMM** The scripts for "1. ED models and SMMs: fixed data".
- - RevBayes scripts for tree inference (and marginal likelihood calculation) with expanded ED models and SMM under fixed data.
- **3_ED_TailColor_problem** The scripts for "3. ED and Tail Color Problem".
- - RevBayes scripts to test the resolution of LTC in the tail color problem under fixed data.
- **4a_EDvsHMM_topology** The scripts for "2. ED models vs. SMMs: simulated data".
- - R scripts (in *RB_run_1/4a_R*) to simulate trees and characters under the ED6 model.
- - RevBayes scripts to perform tree inferences under the ED6, ED3, and two SMMs.
- - R scripts (in *RB_run_1/4a_R*) to calculate boostrapped p-values.
# References
Tarasov, S., 2023. New phylogenetic Markov models for inapplicable morphological characters. *Systematic Biology*, 72(3), pp.681-693.
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