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aphylo
View on CRAN: Click
here
Download and install aphylo package within the R console
Install from CRAN:
install.packages("aphylo")
Install from Github:
library("remotes")
install_github("cran/aphylo")
Install by package version:
library("remotes")
install_version("aphylo", "0.3-4")
Attach the package and use:
library("aphylo")
Maintained by
George Vega Yon
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
10.32614/CRAN.package.aphylo . https://github.com/USCbiostats/aphylo/issues . https://github.com/USCbiostats/aphylo . aphylo citation info . aphylo results . aphylo.pdf . aphylo_0.3-4.tar.gz . aphylo_0.3-4.zip . aphylo_0.3-4.zip . aphylo_0.3-4.zip . aphylo_0.3-4.tgz . aphylo_0.3-4.tgz . aphylo_0.3-4.tgz . aphylo_0.3-4.tgz . aphylo_0.3-4.tgz . aphylo_0.3-4.tgz . aphylo archive . https://CRAN.R-project.org/package=aphylo .
First Published: 2022-01-21
Latest Update: 2023-08-14
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).
How to cite:
George Vega Yon (2022). aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees. R package version 0.3-4, https://cran.r-project.org/web/packages/aphylo. Accessed 29 Mar. 2025.
Previous versions and publish date:
Other packages that cited aphylo R package
View aphylo citation profile
Other R packages that aphylo depends,
imports, suggests or enhances
Complete documentation for aphylo
Functions, R codes and Examples using
the aphylo R package
Some associated functions: LogLike . accuracy_sifter . ape-methods . aphylo-class . aphylo-index . aphylo-info . aphylo-methods . aphylo-model . aphylo-package . aphylo_cv . aphylo_estimates . aphylo_from_data_frame . aphylo_mcmc . aphylo_mle . as.phylo . auc . balance_ann . bprior . fakeexperiment . faketree . imputate_duplications . list_offspring . mislabel . multiAphylo . new_aphylo_pruner . panther-tree . plot.aphylo_prediction_score . plot_logLik . plot_multivariate . posterior-probabilities . prediction_score . raphylo . rdrop_annotations . read_nhx . read_pli . sim_fun_on_tree . sim_tree . states . write_pli .
Some associated R codes: RcppExports.R . accuracy_sifter.R . ape.R . aphylo-ape-info.R . aphylo-package.R . aphylo_from_data_frame.R . aphylo_mcmc.R . aphylo_mle.R . balance.R . color-palettes.R . cv.R . data-management.R . estimation.R . formulas.R . impute_duplications.R . indexing.R . list_offspring.R . loglike.R . multiaphylo.R . panther.R . plot.R . plot_logLik.R . predict.R . prediction_score.R . priors.R . prune.R . read_nhx.R . read_sifter.R . simulation.R . Full aphylo package functions and examples
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