aphylo-info

Nann

Nannotated

Ntrees

Information about annotations, in particular, number of annotations (<code>Nann</code>),
number of annotated leaves (<code>Nannotated</code>), number of unnanotated leaves
(<code>Nunannotated</code>), and number of trees (<code>Ntrees</code>).

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 

aphylo-info function

<dl><dt>phy</dt>
<dd>Either an object of class aphylo, multiAphylo, or
aphylo_estimates.</dd></dl>

Arguments

Information about aphylo and multiAphylo objects — aphylo-info

<dl>

<dt>phy</dt>
<dd>Either an object of class aphylo, multiAphylo, or
aphylo_estimates.</dd>

</dl>

aphylo-info: Information about `aphylo` and `multiAphylo` objects

Description

Usage

Value

Arguments

See Also

Examples