Islands vignette

[ms609]

I had half a vignette in tree-islands.Rmd.

Work out whether this needs completing or whether it's redundant to Islands.Rd

---
title: "Finding islands of phylogenetic trees"
author: "[Martin R. Smith](https://smithlabdurham.github.io/)"
output: 
  rmarkdown::html_vignette:
    fig_width: 6
    fig_height: 4
bibliography: ../inst/REFERENCES.bib
csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
vignette: >
  %\VignetteIndexEntry{Finding islands of phylogenetic trees}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Collections of phylogenetic trees, such as those output by Bayesian or parsimony
analysis, may occupy discrete regions of tree space such that individual
clusters of trees are separated from all other trees by a certain distance.
Finding such islands, and taking their consensus, can be an effective way
of summarising conflicting signal in a phylogenetic dataset [@Silva2021].

```{r col-trees-by-score}
# Load required libraries
library("TreeTools", quietly = TRUE)
library("TreeDist")

# Generate a set of trees
trees <- as.phylo(as.TreeNumber(BalancedTree(16)) + 0:100 - 15, 16)