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ms609 committed Aug 22, 2024
1 parent ec6e53f commit 2202379
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2 changes: 2 additions & 0 deletions inst/_pkgdown.yml
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Expand Up @@ -100,6 +100,8 @@ articles:

template:
bootstrap: 5
bslib:
danger: "#A6081A" # Accessibility suggestion
params:
bootswatch: cerulean
docsearch:
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6 changes: 6 additions & 0 deletions vignettes/Using-TreeDist.Rmd
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Expand Up @@ -89,6 +89,9 @@ rely on matching each split within a tree with another split in the other tree.
We can view an optimal matching:

```{r visualise-matching, fig.align='center', fig.width=8, out.width='90%'}
#| fig.alt: >
#| Pair of similar phylogenetic trees with matched splits highlighted
#| according to the amount of clustering information in common.
VisualizeMatching(ClusteringInfoDistance, tree1, tree2)
```

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original tree:

```{r named-splits, fig.align='center', fig.width=7, fig.height = 5, out.width='80%'}
#| fig.alt: >
#| Phylogenetic tree with nodes numbered, and labelled with the splits
#| to which they correspond.
oldPar <- par(mar = rep(0, 4))
plot(tree2)
ape::nodelabels()
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