Package: aphylo 0.3-4

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_0.3-4.tar.gz
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aphylo.pdf |aphylo.html✨
aphylo/json (API)
NEWS

# Install 'aphylo' in R:
install.packages('aphylo', repos = c('https://uscbiostats.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

annotationsinferencephylogeneticsrcpparmadillo

5.49 score 6 stars 104 scripts 295 downloads 40 exports 12 dependencies

Last updated 1 years agofrom:d11fc14f81. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-win-x86_64NOTENov 11 2024
R-4.5-linux-x86_64NOTENov 11 2024
R-4.4-win-x86_64NOTENov 11 2024
R-4.4-mac-x86_64NOTENov 11 2024
R-4.4-mac-aarch64NOTENov 11 2024
R-4.3-win-x86_64OKNov 11 2024
R-4.3-mac-x86_64OKNov 11 2024
R-4.3-mac-aarch64OKNov 11 2024

Exports:accuracy_sifteraphylo_cvAPHYLO_DEFAULT_MCMC_CONTROLaphylo_formulaaphylo_from_data_frameaphylo_mcmcaphylo_mleAPHYLO_PARAM_DEFAULTaucbalance_annbpriordist2rootget_postorderimputate_duplicationslist_offspringlist_parentsLogLikemislabelNannNannotatednew_aphylonew_aphylo_prunerNtreesplot_logLikplot_multivariatepredict_brute_forcepredict_pre_orderprediction_scoreraphylordrop_annotationsread_nhxread_pantherread_pliread.pantherrmultiAphylosim_fun_on_treesim_treestatesupriorwrite_pli

Dependencies:apeclicodadigestfmcmclatticeMASSMatrixnlmeRcpprlangxml2

Simulation and Inference

George G. Vega Yon

Rendered fromexample.Rmdusingknitr::rmarkdownon Nov 11 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Statistical Inference in Annotated Phylogenetic Treesaphylo-package
Accuracy calculation as defined in Engelhardt et al. (2011)accuracy_sifter accuracy_sifter.aphylo_estimates accuracy_sifter.default
Available methods from the APE packageape-methods
Leave-one-out Cross Validationaphylo_cv aphylo_cv.formula
Model estimation using Markov Chain Monte CarloAPHYLO_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 annotationsaphylo_from_data_frame
Model estimation using Maximum Likelihood Estimationaphylo_mle MLE
Annotated Phylogenetic Treeaphylo aphylo-class new_aphylo new_aphylo.phylo
Indexing aphylo objectsaphylo-index [.aphylo [<-.aphylo
Information about 'aphylo' and 'multiAphylo' objectsaphylo-info Nann Nannotated Ntrees
Plot and print methods for 'aphylo' objectsaphylo-methods plot.aphylo
Formulas in 'aphylo'aphylo-formula aphylo-model aphylo_formula eta mu_d mu_s Pi psi
Extensions to the 'as.phylo' functionas.phylo as.phylo.aphylo as.phylo.matrix
Area Under the Curve and Receiving Operating Curveauc plot.aphylo_auc print.aphylo_auc
Functional balance of a treebalance_ann
Default priors for aphylo_mcmcbprior uprior
Pointer to 'pruner'aphylo_pruner dist2root get_postorder new_aphylo_pruner
Fake Experimental Datafakeexperiment
Fake Phylogenetic Treefaketree
Impute duplication events based on a vector of speciesimputate_duplications
List each nodes' offspring or parentlist_offspring list_parents
Likelihood of an observed annotated phylogenetic treeLogLike
Switch labels acoording to mislabeling probabilitiesmislabel
Building Lists of Annotated Treesc.aphylo multiAphylo print.multiAphylo
Reads PANTHER db treesPANTHER panther-tree PANTHERDB read.panther read_panther
Plot Log-Likelihood function of the modelplot_logLik plot_logLik.aphylo plot_logLik.aphylo_estimates plot_logLik.formula
Multiavariate plot (surface)plot_multivariate
Visualize predictionsplot-prediction plot.aphylo_prediction_score
Posterior probabilities based on parameter estimatesposterior-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 Treesraphylo rmultiAphylo
Randomly drop leaf annotationsrdrop_annotations
Read New Hampshire eXtended format for treesread_nhx
Read PLI files from SIFTERread_pli
Simulate functions on a ginven treesim_fun_on_tree
Random tree generationsim_tree
Matrix of statesstates
Write pli files used by SIFTERwrite_pli