NormalizeInfo

unnormalized

Trees from which <code>unnormalized</code> was calculated

tree1, tree2

Function to calculate the information content of each tree

InfoInTree

Numeric specifying information content of both trees
independently (optional)

infoInBoth

Additional parameters to <code>InfoInTree()</code> or <code>how</code>.

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Function that takes as inputs <code>tree1Info</code> and <code>tree2Info</code>, and
returns a normalizing constant against which to divide <code>unnormalized</code>.

Func

Normalize information against total present in both starting trees

internal

Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Calculates the median of a set of trees under any distance metric.

NormalizeInfo: Normalize information against total present in both starting trees

Description

Usage

Arguments