AllSPR

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

AllSPR function

<dl><dt>parent</dt>
<dd>Integer vector corresponding to the first column of the edge
matrix of a tree of class <code>phylo</code>, i.e. <code>tree$edge[, 1]</code>.</dd>
<dt>child</dt>
<dd>Integer vector corresponding to the second column of the edge
matrix of a tree of class <code>phylo</code>, i.e. <code>tree$edge[, 2]</code>.</dd>
<dt>nEdge</dt>
<dd>integer specifying the number of edges of a tree of class <code>phylo</code>, i.e. <code>dim(tree$edge)[1]</code></dd>
<dt>notDuplicateRoot</dt>
<dd>logical vector of length <code>nEdge</code>, specifying for each
edge whether it is the second edge leading to the root (in which case
its breaking will be equivalent to breaking the other root edge...
except insofar as it moves the position of the root.)</dd>
<dt>edgeToBreak</dt>
<dd>(optional) integer specifying the index of an edge to bisect/prune,
generated randomly if not specified.
Alternatively, set to <code>-1</code> to return a complete list
of all trees one step from the input tree.</dd></dl>

Arguments

Author

All SPR trees — AllSPR

<dl>

<dt>parent</dt>
<dd>Integer vector corresponding to the first column of the edge
matrix of a tree of class <code>phylo</code>, i.e. <code>tree$edge[, 1]</code>.</dd>


<dt>child</dt>
<dd>Integer vector corresponding to the second column of the edge
matrix of a tree of class <code>phylo</code>, i.e. <code>tree$edge[, 2]</code>.</dd>


<dt>nEdge</dt>
<dd>integer specifying the number of edges of a tree of class <code>phylo</code>, i.e. <code>dim(tree$edge)[1]</code></dd>


<dt>notDuplicateRoot</dt>
<dd>logical vector of length <code>nEdge</code>, specifying for each
edge whether it is the second edge leading to the root (in which case
its breaking will be equivalent to breaking the other root edge...
except insofar as it moves the position of the root.)</dd>


<dt>edgeToBreak</dt>
<dd>(optional) integer specifying the index of an edge to bisect/prune,
generated randomly if not specified.
Alternatively, set to <code>-1</code> to return a complete list
of all trees one step from the input tree.</dd>

</dl>

AllSPR: All SPR trees

Description

Usage

Value

Arguments

Author