Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/phylo.diff.R View source: R/mcmc.target.seq.R

A family of functions for determining and plotting the differences between two trees.

`phylo.diff`

plots two trees side by side, highlighting edges unique
to each tree in red.

`distinct.edges`

finds the edges present in the first argument not in
the second.

`edge.from.split`

locates the edge id from a given split.

`get.bipartition`

gets the bipartition of tips formed by a single edge.

`partition.leaves`

returns the set of all bipartitions from all edges.

1 2 3 4 5 6 7 8 9 | ```
phylo.diff(x, y, ...)
distinct.edges(x, y)
edge.from.split(x, split)
get.bipartition(x, e)
partition.leaves(x)
``` |

`x` |
The first (or only) tree. |

`y` |
The second tree, for the functions that accept two trees. |

`split` |
A list of bipartitions, probably from |

`e` |
An edge for a particular tree, given as an id. |

`...` |
Additional arguments to pass to the |

`phylo.diff`

uses the ape tree plotting function. The other functions
are mostly meant as support functions.

`phylo.diff`

returns invisible.

`distinct.edges`

returns a numeric vector of edge ids for the first
tree.

`edge.from.split`

returns an edge id for a particular tree
corresponding to a given bipartition and NA if none such edge exists.

`get.bipartition`

returns a character vector of the tips below that
edge in the given tree.

`partition.leaves`

returns a list of partitions (themselves character
vectors) of the given tree.

John Chakerian <[email protected]>

Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
data(woodmouse)
otree <- root(fastme.ols(dist.dna(woodmouse)), "No305", resolve.root=TRUE)
breps = 10
trees <- boot.phylo(otree, woodmouse, B=breps, function(x)
root(fastme.ols(dist.dna(x)), "No305", resolve.root=TRUE),trees=TRUE)
combined.trees <- c(list(otree), trees$trees)
binning <- bin.multiPhylo(combined.trees)
phylo.diff(combined.trees[[match(1, binning)]], combined.trees[[match(2, binning)]])
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.