fakeexperiment

A fake dataset containing 2 functional state of the leaf nodes. Each
function can have either 0 (unactive), 1 (active) or 9 (n/a).
This dataset is inteded for testing only.

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 

fakeexperiment function

A data frame with 4 rows and 3 variables:<dl>
<dt>f1</dt>
<dd>State of function 1.</dd><dt>f2</dt>
<dd>State of function 1.</dd><dt>LeafId</dt>
<dd>Integer, ID of the leaf.</dd>
</dl>

Format

Fake Experimental Data — fakeexperiment

A data frame with 4 rows and 3 variables:<dl>
<dt>f1</dt>
<dd>State of function 1.</dd>

<dt>f2</dt>
<dd>State of function 1.</dd>

<dt>LeafId</dt>
<dd>Integer, ID of the leaf.</dd>


</dl>

fakeexperiment: Fake Experimental Data

Description

Arguments

Format