{ "_id": "6a101c5aacfb0bcc41c87b17", "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://phylotastic.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": "2026-05-14 08:30:04 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": "a78a5e766f27af7dea0178e0da3ffdfa", "_user": "phylotastic", "_type": "src", "_file": "aphylo_0.3-6.tar.gz", "_fileid": "217948bddf7b946f1234200bef52270ade19ecdc8f3f25fff09d35fa0fd22513", "_filesize": 1698665, "_sha256": "217948bddf7b946f1234200bef52270ade19ecdc8f3f25fff09d35fa0fd22513", "_created": "2026-05-14T08:30:04.000Z", "_published": "2026-05-22T09:05:30.217Z", "_distro": "noble", "_jobs": [ { "job": 77349216603, "time": 185, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "6990406391" }, { "job": 77349216596, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6990406874" }, { "job": 77349217472, "time": 202, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6990410718" }, { "job": 77349216875, "time": 184, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6990406367" }, { "job": 77349217043, "time": 200, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6990409949" }, { "job": 77349217022, "time": 315, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "6990441599" }, { "job": 77349217065, "time": 186, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6990406727" }, { "job": 77349216595, "time": 238, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6990420387" }, { "job": 77349216017, "time": 246, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6990356269" }, { "job": 77349216040, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156826681" }, { "job": 77349216908, "time": 188, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6990407180" }, { "job": 77349217197, "time": 188, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6990407382" }, { "job": 77349216593, "time": 221, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6990416143" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25850019162", "_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", "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": false, "_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": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 610, "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' 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