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