states

Implements a parsimonious evolutionary model to analyze and
predict gene-functional annotations in phylogenetic trees as described in Vega
Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on
computational efficiency, 'aphylo' makes it possible to estimate pooled
phylogenetic models, including thousands (hundreds) of annotations (trees) in
the same run. The package also provides the tools for visualization of
annotated phylogenies, calculation of posterior probabilities (prediction)
and goodness-of-fit assessment featured in Vega Yon et al. (2021).

George Vega Yon

aphylo

Statistical Inference and Prediction of Annotations in
Phylogenetic Trees

National
Cancer Institute (NCI) 

USC Biostatistics 

states function

<dl><dt>P</dt>
<dd>Integer scalar. Number of functions.</dd></dl>

Arguments

Matrix of states — states

<dl>

<dt>P</dt>
<dd>Integer scalar. Number of functions.</dd>

</dl>

states: Matrix of states

Description

Usage

Value

Arguments

Examples