WhenFirstHit

Reports when each tree in a list was first found by tree search.
This information is read from the <code>firstHit</code> attribute if present.
If not, trees are taken to be listed in the order in which they were found,
and named according to the search iteration in which they were first hit -
the situation when trees found by <code>MaximizeParsimony()</code> are saved to file.

Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.

Martin R. Smith

TreeSearch

Phylogenetic Analysis with Discrete Character Data

Martin Brazeau

WhenFirstHit function

<dl><dt>trees</dt>
<dd>A list of trees, or a <code>multiPhylo</code> object.</dd></dl>

Arguments

<a href="https://smithlabdurham.github.io/">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeSearch&version=1.6.1" data-mini-rdoc="TreeSearch::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

When was a tree topology first hit? — WhenFirstHit

<dl>

<dt>trees</dt>
<dd>A list of trees, or a <code>multiPhylo</code> object.</dd>

</dl>

<a href='https://smithlabdurham.github.io/'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

WhenFirstHit: When was a tree topology first hit?

Description

Usage

Value

Arguments

Author

See Also

Examples