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aphylo (version 0.3-4)

Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Description

Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) . 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).

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Install

install.packages('aphylo')

Monthly Downloads

306

Version

0.3-4

License

MIT + file LICENSE

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Repository

https://github.com/USCbiostats/aphylo

Maintainer

George Vega Yon

Last Published

December 3rd, 2024

Functions in aphylo (0.3-4)

APHYLO_DEFAULT_MCMC_CONTROL

Model estimation using Markov Chain Monte Carlo

rdrop_annotations

Randomly drop leaf annotations

Read New Hampshire eXtended format for trees

Pointer to pruner

Model estimation using Maximum Likelihood Estimation

Reads PANTHER db trees

prediction_score

Calculate prediction score (quality of prediction)

plot_multivariate

Multiavariate plot (surface)

List each nodes' offspring or parent

Write pli files used by SIFTER

Simulation of Annotated Phylogenetic Trees

posterior-probabilities

Posterior probabilities based on parameter estimates

Building Lists of Annotated Trees

Matrix of states

imputate_duplications

Impute duplication events based on a vector of species

Read PLI files from SIFTER

sim_fun_on_tree

Simulate functions on a ginven tree

plot.aphylo_prediction_score

Visualize predictions

Random tree generation

Plot Log-Likelihood function of the model

Indexing aphylo objects

Available methods from the APE package

Likelihood of an observed annotated phylogenetic tree

Leave-one-out Cross Validation

Plot and print methods for aphylo objects

Statistical Inference in Annotated Phylogenetic Trees

accuracy_sifter

Accuracy calculation as defined in Engelhardt et al. (2011)

Annotated Phylogenetic Tree

Information about aphylo and multiAphylo objects

Formulas in aphylo

Extensions to the as.phylo function

Default priors for aphylo_mcmc

Fake Experimental Data

Area Under the Curve and Receiving Operating Curve

Fake Phylogenetic Tree

Functional balance of a tree

aphylo_from_data_frame

Create an aphylo object with partial annotations

aphylo_estimates

Objects of class aphylo_estimates

Switch labels acoording to mislabeling probabilities