mpl_attach_rawdata

Attaches a raw data character state matrix in the form of a C-style
(i.e. NULL-terminated) string. This can be the matrix block extracted from a
Nexus file or an <code>xread</code> table format.
The matrix should contain no leaf labels.

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_attach_rawdata function

<dl><dt>rawdata</dt>
<dd>C-style string corresponding to the tip data for each taxon in
turn.</dd>
<dt>morphyobj</dt>
<dd>An instance of the Morphy object.</dd></dl>

Arguments

Author

Attach raw character state data (i.e. tip data). — mpl_attach_rawdata

<dl>

<dt>rawdata</dt>
<dd>C-style string corresponding to the tip data for each taxon in
turn.</dd>


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

</dl>

mpl_attach_rawdata: Attach raw character state data (i.e. tip data).

Description

Usage

Value

Arguments

Author

See Also