This package is considered a duplicate. The official version of this package is found at:https://uscbiostats.r-universe.dev/aphylo

Package: aphylo 0.3-6

George Vega Yon

aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

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).

Authors:George Vega Yon [aut, cre], National Cancer Institute [fnd], USC Biostatistics [cph]

aphylo_0.3-6.tar.gz
aphylo_0.3-6.zip(r-4.7)aphylo_0.3-6.zip(r-4.6)aphylo_0.3-6.zip(r-4.5)
aphylo_0.3-6.tgz(r-4.6-x86_64)aphylo_0.3-6.tgz(r-4.6-arm64)aphylo_0.3-6.tgz(r-4.5-x86_64)aphylo_0.3-6.tgz(r-4.5-arm64)
aphylo_0.3-6.tar.gz(r-4.7-arm64)aphylo_0.3-6.tar.gz(r-4.7-x86_64)aphylo_0.3-6.tar.gz(r-4.6-arm64)aphylo_0.3-6.tar.gz(r-4.6-x86_64)
aphylo_0.3-6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
aphylo/json (API)

# Install 'aphylo' in R:

install.packages('aphylo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uscbiostats/aphylo/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

fakeexperiment - Fake Experimental Data
faketree - Fake Phylogenetic Tree

On CRAN:

annotations inference phylogenetics rcpparmadillo cpp

6.45 score 6 stars 95 scripts 624 downloads 40 exports 12 dependencies

Last updated from:beef2b5b07. Checks:13 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	201
linux-devel-x86_64	OK	212
source / vignettes	OK	213
linux-release-arm64	OK	199
linux-release-x86_64	OK	238
macos-release-arm64	OK	126
macos-release-x86_64	OK	259
macos-oldrel-arm64	OK	131
macos-oldrel-x86_64	OK	370
windows-devel	OK	182
windows-release	OK	177
windows-oldrel	OK	173
wasm-release	OK	130

Exports:accuracy_sifter aphylo_cv APHYLO_DEFAULT_MCMC_CONTROL aphylo_formula aphylo_from_data_frame aphylo_mcmc aphylo_mle APHYLO_PARAM_DEFAULT auc balance_ann bprior dist2root get_postorder imputate_duplications list_offspring list_parents LogLike mislabel Nann Nannotated new_aphylo new_aphylo_pruner Ntrees plot_logLik plot_multivariate predict_brute_force predict_pre_order prediction_score raphylo rdrop_annotations read_nhx read_panther read_pli read.panther rmultiAphylo sim_fun_on_tree sim_tree states uprior write_pli

Dependencies:ape cli coda digest fmcmc lattice MASS Matrix nlme Rcpp rlang xml2

Simulation and Inference

Setup | Simulation | Inference

Rendered fromexample.Rmdusingknitr::rmarkdown

Last update: 2021-11-09
Started: 2021-08-18

Help page	Topics
Statistical Inference in Annotated Phylogenetic Trees	aphylo-package
Accuracy calculation as defined in Engelhardt et al. (2011)	accuracy_sifter accuracy_sifter.aphylo_estimates accuracy_sifter.default
Available methods from the APE package	ape-methods
Leave-one-out Cross Validation	aphylo_cv aphylo_cv.formula
Model estimation using Markov Chain Monte Carlo	APHYLO_DEFAULT_MCMC_CONTROL aphylo_mcmc APHYLO_PARAM_DEFAULT MCMC
Objects of class 'aphylo_estimates'	aphylo_estimates coef.aphylo_estimates plot.aphylo_estimates print.aphylo_estimates vcov.aphylo_estimates
Create an 'aphylo' object with partial annotations	aphylo_from_data_frame
Model estimation using Maximum Likelihood Estimation	aphylo_mle MLE
Annotated Phylogenetic Tree	aphylo aphylo-class new_aphylo new_aphylo.phylo
Indexing aphylo objects	aphylo-index [.aphylo [<-.aphylo
Information about 'aphylo' and 'multiAphylo' objects	aphylo-info Nann Nannotated Ntrees
Plot and print methods for 'aphylo' objects	aphylo-methods plot.aphylo
Formulas in 'aphylo'	aphylo-formula aphylo-model aphylo_formula eta mu_d mu_s Pi psi
Extensions to the 'as.phylo' function	as.phylo as.phylo.aphylo as.phylo.matrix
Area Under the Curve and Receiving Operating Curve	auc plot.aphylo_auc print.aphylo_auc
Functional balance of a tree	balance_ann
Default priors for aphylo_mcmc	bprior uprior
Pointer to 'pruner'	aphylo_pruner dist2root get_postorder new_aphylo_pruner
Fake Experimental Data	fakeexperiment
Fake Phylogenetic Tree	faketree
Impute duplication events based on a vector of species	imputate_duplications
List each nodes' offspring or parent	list_offspring list_parents
Likelihood of an observed annotated phylogenetic tree	LogLike
Switch labels acoording to mislabeling probabilities	mislabel
Building Lists of Annotated Trees	c.aphylo multiAphylo print.multiAphylo
Reads PANTHER db trees	PANTHER panther-tree PANTHERDB read.panther read_panther
Plot Log-Likelihood function of the model	plot_logLik plot_logLik.aphylo plot_logLik.aphylo_estimates plot_logLik.formula
Multiavariate plot (surface)	plot_multivariate
Visualize predictions	plot-prediction plot.aphylo_prediction_score
Posterior probabilities based on parameter estimates	posterior-probabilities predict.aphylo_estimates predict_brute_force predict_pre_order predict_pre_order.aphylo predict_pre_order.aphylo_estimates
Calculate prediction score (quality of prediction)	prediction_score prediction_score.aphylo_estimates print.aphylo_prediction_score
Simulation of Annotated Phylogenetic Trees	raphylo rmultiAphylo
Randomly drop leaf annotations	rdrop_annotations
Read New Hampshire eXtended format for trees	read_nhx
Read PLI files from SIFTER	read_pli
Simulate functions on a ginven tree	sim_fun_on_tree
Random tree generation	sim_tree
Matrix of states	states
Write pli files used by SIFTER	write_pli

Package: aphylo 0.3-6

aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

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Help Manual

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