mpl_init_Morphy

Provides initial dimensions for the dataset, which will
constrain any input matrix supplied to Morphy.

internal

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

mpl_init_Morphy function

<dl><dt>numtaxa</dt>
<dd>The number of taxa (or tips/terminals).</dd>
<dt>numchars</dt>
<dd>The number of characters (i.e. transformation series) in the
data set.</dd>
<dt>morphyobj</dt>
<dd>An instance of the Morphy object.</dd></dl>

Arguments

Author

Sets up the dimensions of the dataset. — mpl_init_Morphy

<dl>

<dt>numtaxa</dt>
<dd>The number of taxa (or tips/terminals).</dd>


<dt>numchars</dt>
<dd>The number of characters (i.e. transformation series) in the
data set.</dd>


<dt>morphyobj</dt>
<dd>An instance of the Morphy object.</dd>

</dl>

mpl_init_Morphy: Sets up the dimensions of the dataset.

Description

Usage

Value

Arguments

Author

See Also