{ "_id": "6a1164e2acfb0bcc41cefd14", "Package": "aphylo", "Title": "Statistical Inference and Prediction of Annotations in\nPhylogenetic Trees", "Authors@R": "c(person(\"George\", \"Vega Yon\", role=c(\"aut\",\"cre\"),\nemail=\"g.vegayon@gmail.com\", comment = c(ORCID = \"0000-0002-3171-0844\")),\nperson(\"National\nCancer Institute (NCI)\", role = \"fnd\", comment = \"Grant Number\n5P01CA196569-02\"),\nperson(\"USC Biostatistics\", role = \"cph\")\n)", "Version": "0.3-6", "Description": "Implements a parsimonious evolutionary model to analyze\nand predict gene-functional annotations in phylogenetic trees\nas described in Vega Yon et al. (2021)\n. Focusing on computational\nefficiency, 'aphylo' makes it possible to estimate pooled\nphylogenetic models, including thousands (hundreds) of\nannotations (trees) in the same run. The package also provides\nthe tools for visualization of annotated phylogenies,\ncalculation of posterior probabilities (prediction) and\ngoodness-of-fit assessment featured in Vega Yon et al. (2021).", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "URL": "https://github.com/USCbiostats/aphylo", "BugReports": "https://github.com/USCbiostats/aphylo/issues", "Classification/MSC": "90C35, 90B18, 91D30", "License": "MIT + file LICENSE", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "libxml2-dev", "Repository": "https://uscbiostats.r-universe.dev", "Date/Publication": "2026-01-14 10:57:44 UTC", "RemoteUrl": "https://github.com/uscbiostats/aphylo", "RemoteRef": "HEAD", "RemoteSha": "beef2b5b07a6f6e5e1963f0ac9976e8f3ff7c64b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-23 08:21:52 UTC", "User": "root" }, "Author": "George Vega Yon [aut, cre] (ORCID:\n),\nNational Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),\nUSC Biostatistics [cph]", "Maintainer": "George Vega Yon ", "MD5sum": "70cc3167200dd8aa39b930f2dac0a862", "_user": "uscbiostats", "_type": "src", "_file": "aphylo_0.3-6.tar.gz", "_fileid": "1cc468692fe5283be86b690e3327d4b8779ba7c5b843dce98c3dfa56b7f9f676", "_filesize": 1698694, "_sha256": "1cc468692fe5283be86b690e3327d4b8779ba7c5b843dce98c3dfa56b7f9f676", "_created": "2026-05-23T08:21:52.000Z", "_published": "2026-05-23T08:27:14.880Z", "_distro": "noble", "_jobs": [ { "job": 77509087990, "time": 183, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7175617914" }, { "job": 77509087994, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175618355" }, { "job": 77509087997, "time": 185, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175618081" }, { "job": 77509088010, "time": 190, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175618602" }, { "job": 77509088018, "time": 122, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175612829" }, { "job": 77509087998, "time": 232, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7175622072" }, { "job": 77509088000, "time": 108, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175611851" }, { "job": 77509087996, "time": 258, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175624217" }, { "job": 77508859239, "time": 255, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175602057" }, { "job": 77509087978, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175611839" }, { "job": 77509087993, "time": 190, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175618574" }, { "job": 77509088015, "time": 160, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175615926" }, { "job": 77509087992, "time": 195, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175619010" } ], "_buildurl": "https://github.com/r-universe/uscbiostats/actions/runs/26327910065", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/uscbiostats/aphylo", "_commit": { "id": "beef2b5b07a6f6e5e1963f0ac9976e8f3ff7c64b", "author": "George G. Vega Yon ", "committer": "GitHub ", "message": "Accepted on CRAN (fixes documentation) (#29)\n\n", "time": 1768388264 }, "_maintainer": { "name": "George Vega Yon", "email": "g.vegayon@gmail.com", "login": "gvegayon", "bluesky": "@gvegayon.bsky.social", "linkedin": "in/georgevegayon", "description": "Scientist at @UofUEpiBio modeling complex systems using statistical computing. Lots of time at @CDCgov.", "uuid": 893619, "orcid": "0000-0002-3171-0844" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "ape", "version": ">= 5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.1", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "fmcmc", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "AUC", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "uscbiostats", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-36", "n": 2 }, { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-47", "n": 1 }, { "week": "2026-03", "n": 1 } ], "_tags": [ { "name": "v0.3-5", "date": "2025-11-20" }, { "name": "v0.3-6", "date": "2026-01-14" } ], "_topics": [ "annotations", "inference", "phylogenetics", "rcpparmadillo", "cpp" ], "_stars": 6, "_contributors": [ { "user": "gvegayon", "count": 350, "uuid": 893619 }, { "user": "copilot", "count": 3, "uuid": 198982749 }, { "user": "immaterial0", "count": 1, "uuid": 11642347 } ], "_userbio": { "uuid": 10712919, "type": "organization", "name": "USC Division of Biostatistics", "description": "Organization for USC Division of Biostatistics" }, "_downloads": { "count": 646, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aphylo" }, "_devurl": "https://github.com/uscbiostats/aphylo", "_searchresults": 104, "_rbuild": "4.6.0", "_assets": [ "extra/aphylo.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/uscbiostats/aphylo", "_realowner": "uscbiostats", "_cranurl": true, "_releases": [ { "version": "0.2-1", "date": "2022-01-21" }, { "version": "0.3-1", "date": "2022-12-20" }, { "version": "0.3-2", "date": "2022-12-21" }, { "version": "0.3-3", "date": "2023-09-07" }, { "version": "0.3-4", "date": "2024-12-03" }, { "version": "0.3-5", "date": "2025-11-20" }, { "version": "0.3-6", "date": "2026-01-09" } ], "_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" ], "_datasets": [ { "name": "fakeexperiment", "title": "Fake Experimental Data", "object": "fakeexperiment", "class": [ "matrix", "array" ], "fields": [ "LeafId", "f1", "f2" ], "rows": 4, "table": true, "tojson": true }, { "name": "faketree", "title": "Fake Phylogenetic Tree", "object": "faketree", "class": [ "matrix", "array" ], "fields": [ "ParentId", "NodeId" ], "rows": 6, "table": true, "tojson": true } ], "_help": [ { "page": "aphylo-package", "title": "Statistical Inference in Annotated Phylogenetic Trees", "topics": [ "aphylo-package" ] }, { "page": "accuracy_sifter", "title": "Accuracy calculation as defined in Engelhardt et al. (2011)", "topics": [ "accuracy_sifter", "accuracy_sifter.aphylo_estimates", "accuracy_sifter.default" ] }, { "page": "ape-methods", "title": "Available methods from the APE package", "concept": [ "information" ], "topics": [ "ape-methods" ] }, { "page": "aphylo_cv", "title": "Leave-one-out Cross Validation", "topics": [ "aphylo_cv", "aphylo_cv.formula" ] }, { "page": "aphylo_mcmc", "title": "Model estimation using Markov Chain Monte Carlo", "concept": [ "parameter estimation" ], "topics": [ "APHYLO_DEFAULT_MCMC_CONTROL", "aphylo_mcmc", "APHYLO_PARAM_DEFAULT", "MCMC" ] }, { "page": "aphylo_estimates", "title": "Objects of class 'aphylo_estimates'", "topics": [ "aphylo_estimates", "coef.aphylo_estimates", "plot.aphylo_estimates", "print.aphylo_estimates", "vcov.aphylo_estimates" ] }, { "page": "aphylo_from_data_frame", "title": "Create an 'aphylo' object with partial annotations", "concept": [ "Data management functions" ], "topics": [ "aphylo_from_data_frame" ] }, { "page": "aphylo_mle", "title": "Model estimation using Maximum Likelihood Estimation", "concept": [ "parameter estimation" ], "topics": [ "aphylo_mle", "MLE" ] }, { "page": "aphylo-class", "title": "Annotated Phylogenetic Tree", "concept": [ "Data management functions", "aphylo methods" ], "topics": [ "aphylo", "aphylo-class", "new_aphylo", "new_aphylo.phylo" ] }, { "page": "aphylo-index", "title": "Indexing aphylo objects", "topics": [ "aphylo-index", "[.aphylo", "[<-.aphylo" ] }, { "page": "aphylo-info", "title": "Information about 'aphylo' and 'multiAphylo' objects", "concept": [ "information" ], "topics": [ "aphylo-info", "Nann", "Nannotated", "Ntrees" ] }, { "page": "aphylo-methods", "title": "Plot and print methods for 'aphylo' objects", "concept": [ "aphylo methods" ], "topics": [ "aphylo-methods", "plot.aphylo" ] }, { "page": "aphylo-model", "title": "Formulas in 'aphylo'", "topics": [ "aphylo-formula", "aphylo-model", "aphylo_formula", "eta", "mu_d", "mu_s", "Pi", "psi" ] }, { "page": "as.phylo", "title": "Extensions to the 'as.phylo' function", "topics": [ "as.phylo", "as.phylo.aphylo", "as.phylo.matrix" ] }, { "page": "auc", "title": "Area Under the Curve and Receiving Operating Curve", "topics": [ "auc", "plot.aphylo_auc", "print.aphylo_auc" ] }, { "page": "balance_ann", "title": "Functional balance of a tree", "topics": [ "balance_ann" ] }, { "page": "bprior", "title": "Default priors for aphylo_mcmc", "topics": [ "bprior", "uprior" ] }, { "page": "new_aphylo_pruner", "title": "Pointer to 'pruner'", "topics": [ "aphylo_pruner", "dist2root", "get_postorder", "new_aphylo_pruner" ] }, { "page": "fakeexperiment", "title": "Fake Experimental Data", "topics": [ "fakeexperiment" ] }, { "page": "faketree", "title": "Fake Phylogenetic Tree", "topics": [ "faketree" ] }, { "page": "imputate_duplications", "title": "Impute duplication events based on a vector of species", "topics": [ "imputate_duplications" ] }, { "page": "list_offspring", "title": "List each nodes' offspring or parent", "topics": [ "list_offspring", "list_parents" ] }, { "page": "LogLike", "title": "Likelihood of an observed annotated phylogenetic tree", "topics": [ "LogLike" ] }, { "page": "mislabel", "title": "Switch labels acoording to mislabeling probabilities", "topics": [ "mislabel" ] }, { "page": "multiAphylo", "title": "Building Lists of Annotated Trees", "topics": [ "c.aphylo", "multiAphylo", "print.multiAphylo" ] }, { "page": "panther-tree", "title": "Reads PANTHER db trees", "concept": [ "reading" ], "topics": [ "PANTHER", "panther-tree", "PANTHERDB", "read.panther", "read_panther" ] }, { "page": "plot_logLik", "title": "Plot Log-Likelihood function of the model", "topics": [ "plot_logLik", "plot_logLik.aphylo", "plot_logLik.aphylo_estimates", "plot_logLik.formula" ] }, { "page": "plot_multivariate", "title": "Multiavariate plot (surface)", "topics": [ "plot_multivariate" ] }, { "page": "plot.aphylo_prediction_score", "title": "Visualize predictions", "topics": [ "plot-prediction", "plot.aphylo_prediction_score" ] }, { "page": "posterior-probabilities", "title": "Posterior probabilities based on parameter estimates", "topics": [ "posterior-probabilities", "predict.aphylo_estimates", "predict_brute_force", "predict_pre_order", "predict_pre_order.aphylo", "predict_pre_order.aphylo_estimates" ] }, { "page": "prediction_score", "title": "Calculate prediction score (quality of prediction)", "topics": [ "prediction_score", "prediction_score.aphylo_estimates", "print.aphylo_prediction_score" ] }, { "page": "raphylo", "title": "Simulation of Annotated Phylogenetic Trees", "concept": [ "Simulation Functions" ], "topics": [ "raphylo", "rmultiAphylo" ] }, { "page": "rdrop_annotations", "title": "Randomly drop leaf annotations", "topics": [ "rdrop_annotations" ] }, { "page": "read_nhx", "title": "Read New Hampshire eXtended format for trees", "concept": [ "reading" ], "topics": [ "read_nhx" ] }, { "page": "read_pli", "title": "Read PLI files from SIFTER", "concept": [ "reading" ], "topics": [ "read_pli" ] }, { "page": "sim_fun_on_tree", "title": "Simulate functions on a ginven tree", "topics": [ "sim_fun_on_tree" ] }, { "page": "sim_tree", "title": "Random tree generation", "topics": [ "sim_tree" ] }, { "page": "states", "title": "Matrix of states", "topics": [ "states" ] }, { "page": "write_pli", "title": "Write pli files used by SIFTER", "topics": [ "write_pli" ] } ], "_pkglogo": "https://github.com/uscbiostats/aphylo/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/uscbiostats/aphylo/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "coda", "digest", "fmcmc", "lattice", "MASS", "Matrix", "nlme", "Rcpp", "rlang", "xml2" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "example.Rmd", "filename": "example.html", "title": 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