From ec6e53fc98c9cef4fdeec34c2ee7ffded5047b12 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 22 Aug 2024 15:57:13 +0100
Subject: [PATCH] Delete tree-islands.Rmd

---
 vignettes/tree-islands.Rmd | 30 ------------------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 vignettes/tree-islands.Rmd

diff --git a/vignettes/tree-islands.Rmd b/vignettes/tree-islands.Rmd
deleted file mode 100644
index c33810dc..00000000
--- a/vignettes/tree-islands.Rmd
+++ /dev/null
@@ -1,30 +0,0 @@
----
-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)
-
-```
\ No newline at end of file