---
title: "bGMYC4: Package Overview"
author: "Dmitry Karabanov"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{bGMYC4: Package Overview}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Overview

The bGMYC4 package implements a Bayesian version of the
General Mixed Yule-Coalescent model for species delimitation
from single-locus phylogenetic data. It uses Markov Chain
Monte Carlo simulation to evaluate the posterior distribution
of species boundaries and supports flexible prior specification
on model parameters.

## Main functions

- bgmyc.singlephy() - Bayesian GMYC analysis for a single phylogeny
- bgmyc.multiphylo() - Analysis across multiple phylogenies
- bgmyc.dataprep() - Prepare data for analysis
- plot.singlebgmyc() - Visualize results for a single phylogeny
- plot.multibgmyc() - Visualize results across multiple phylogenies

## Vignettes

- Interactive visualization with bGMYC4 (see bGMYC4-interactive.html)

## References

Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A.,
Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D., and
Vogler, A.P. (2006). Sequence-based species delimitation for
the DNA taxonomy of undescribed insects. Systematic Biology,
55(4), 595-609.

Reid, N.M. and Carstens, B.C. (2012). Phylogenetic estimation
error can decrease the accuracy of species delimitation: a
Bayesian implementation of the general mixed Yule-coalescent
model. BMC Evolutionary Biology, 12, 196.