MappingQuality

ProjectionQuality

<code>MappingQuality()</code> calculates the trustworthiness and continuity
of mapped distances Venna2001,Kaski2003TreeDist.
Trustworthiness measures, on a scale from 0--1,
the degree to which points that are nearby in a mapping are truly close
neighbours; continuity, the extent to which points that are truly nearby
retain their close spatial proximity in a mapping.

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>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.

Martin R. Smith

TreeDist

Calculate and Map Distances Between Phylogenetic Trees

Roy Jonker

Yong Yang

Yi Cao

MappingQuality function

<dl><dt>original, mapped</dt>
<dd>Square matrix or <code>dist</code> object containing
original / mapped pairwise distances.</dd>
<dt>neighbours</dt>
<dd>Integer specifying number of nearest neighbours to use in
calculation. This should typically be small relative to the number of
points.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeDist&version=2.9.2" data-mini-rdoc="TreeDist::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Faithfulness of mapped distances — MappingQuality

<dl>

<dt>original, mapped</dt>
<dd>Square matrix or <code>dist</code> object containing
original / mapped pairwise distances.</dd>


<dt>neighbours</dt>
<dd>Integer specifying number of nearest neighbours to use in
calculation. This should typically be small relative to the number of
points.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

MappingQuality: Faithfulness of mapped distances

Description

Usage

Value

Arguments

Author

References

See Also

Examples