{ "_id": "6a10290eacfb0bcc41c912b2", "Package": "tbea", "Title": "Pre- And Post-Processing in Bayesian Evolutionary Analyses", "Version": "1.7.0", "Authors@R": "c(person(\"Gustavo A.\", \"Ballen\", email = \"gustavo.a.ballen@gmail.com\", role = c(\"aut\", \"cre\")), \nperson(\"Sandra\", \"Reinales\", email = \"spreinalesl@gmail.com\", role = c(\"aut\")))", "Description": "Functions are provided for prior specification in\ndivergence time estimation using fossils as well as other kinds\nof data. It provides tools for interacting with the input and\noutput of Bayesian platforms in evolutionary biology such as\n'BEAST2', 'MrBayes', 'RevBayes', or 'MCMCTree'. It Implements a\nsimple measure similarity between probability density functions\nfor comparing prior and posterior Bayesian densities, as well\nas code for calculating the combination of distributions using\nconflation of Hill (2008). Functions for estimating the\norigination time in collections of distributions using the\nx-intercept (e.g., Draper and Smith, 1998) and stratigraphic\nintervals (Marshall 2010) are also available. Hill, T. 2008.\n\"Conflations of probability distributions\". Transactions of the\nAmerican Mathematical Society, 363:3351-3372.\n, Draper, N. R. and Smith, H.\n1998. \"Applied Regression Analysis\". 1--706. Wiley\nInterscience, New York. , Marshall,\nC. R. 2010. \"Using confidence intervals to quantify the\nuncertainty in the end-points of stratigraphic ranges\".\nQuantitative Methods in Paleobiology, 291--316.\n.", "License": "file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "URL": "https://github.com/gaballench/tbea,\nhttps://gaballench.github.io/tbea/", "BugReports": "https://github.com/gaballench/tbea/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Repository": "https://gaballench.r-universe.dev", "Date/Publication": "2025-09-15 13:28:47 UTC", "RemoteUrl": "https://github.com/gaballench/tbea", "RemoteRef": "HEAD", "RemoteSha": "6662fb83a2dc39877121b245a9a2e61e471a19de", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-13 07:40:32 UTC", "User": "root" }, "Author": "Gustavo A. Ballen [aut, cre],\nSandra Reinales [aut]", "Maintainer": "Gustavo A. Ballen ", "MD5sum": "7f94ec24499a03597248d6b02a1f953b", "_user": "gaballench", "_type": "src", "_file": "tbea_1.7.0.tar.gz", "_fileid": "9aacc7685ab326d98d838a91d29e19a0e243329c963ccaccaa4bda728e4d6011", "_filesize": 1813183, "_sha256": "9aacc7685ab326d98d838a91d29e19a0e243329c963ccaccaa4bda728e4d6011", "_created": "2026-05-13T07:40:32.000Z", "_published": "2026-05-22T09:59:42.981Z", "_distro": "noble", "_jobs": [ { "job": 77357508683, "time": 220, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6964335140" }, { "job": 77357508827, "time": 258, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6964346509" }, { "job": 77357508833, "time": 230, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6964330452" }, { "job": 77357508780, "time": 201, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6964320461" }, { "job": 77357508505, "time": 203, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6964268221" }, { "job": 77357508373, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7157831672" }, { "job": 77357508979, "time": 202, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6964328981" }, { "job": 77357508834, "time": 193, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6964326248" }, { "job": 77357508784, "time": 206, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6964330473" } ], "_buildurl": "https://github.com/r-universe/gaballench/actions/runs/25785270936", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/gaballench/tbea", "_commit": { "id": "6662fb83a2dc39877121b245a9a2e61e471a19de", "author": "gaballench ", "committer": "gaballench ", "message": "Updating the readme with the citation information of the paper published\n", "time": 1757942927 }, "_maintainer": { "name": "Gustavo A. Ballen", "email": "gustavo.a.ballen@gmail.com", "login": "gaballench", "twitter": "@gaballench", "uuid": 7208813 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "Rfit", "role": "Imports" }, { "package": "boot", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Kendall", "role": "Suggests" } ], "_owner": "gaballench", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-34", "n": 10 }, { "week": "2025-37", "n": 3 }, { "week": "2025-38", "n": 1 } ], "_tags": [ { "name": "v1.7.0", "date": "2025-08-19" } ], "_stars": 3, "_contributors": [ { "user": "gaballench", "count": 110, "uuid": 7208813 }, { "user": "spreinalesl", "count": 5, "uuid": 11969625 } ], "_userbio": { "uuid": 7208813, "type": "user", "name": "Gustavo A. Ballen", "description": "FAPESP Postdoctoral Fellow @ IBB UNESP Botucatu. Computational phylogenetics, evolutionary biology and cultural evolution. Renaissance lute player." }, "_downloads": { "count": 510, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tbea" }, "_devurl": "https://github.com/gaballench/tbea", "_pkgdown": "https://gaballench.github.io/tbea/", "_searchresults": 22, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/tbea.html", "manual.pdf" ], "_homeurl": "https://github.com/gaballench/tbea", "_realowner": "gaballench", "_cranurl": true, "_releases": [ { "version": "1.4.2", "date": "2024-06-04" }, { "version": "1.5.0", "date": "2024-07-01" }, { "version": "1.6.1", "date": "2025-04-10" }, { "version": "1.7.0", "date": "2025-08-19" } ], "_exports": [ "c_truncauchy", "concatNexus", "conflate", "crossplot", "density_fun", "fasta2nexus", "findParams", "lognormalBeast", "measureSimil", "mswd.test", "quantile_conflation", "stratCI", "summaryBrlen", "table2nexus", "tnt2newick", "topoFreq", "xintercept" ], "_datasets": [ { "name": "andes", "title": "Divergence-time estimation data for cis-trans-Andean pairs", "object": "andes", "class": [ "data.frame" ], "fields": [ "ages", "min", "max" ], "rows": 54, "table": true, "tojson": true }, { "name": "cynodontidae.posterior", "title": "Posterior samples for the family Cynodontidae", "object": "cynodontidae.posterior", "class": [ "data.frame" ], "fields": [ "Sample", "mrca.date.backward.Hydrolycus.", "mrca.date.backward.Cynodontidae.", "mrca.date.backward.Cynodon_Hydrolycus.", "mrca.date.backward.H_scomberoides.", "mrca.date.backward.Cynodon." ], "rows": 1000, "table": true, "tojson": true }, { "name": "cynodontidae.prior", "title": "Prior samples for the family Cynodontidae", "object": "cynodontidae.prior", "class": [ "data.frame" ], "fields": [ "Sample", "mrca.date.backward.Hydrolycus.", "mrca.date.backward.Cynodontidae.", "mrca.date.backward.Cynodon_Hydrolycus.", "mrca.date.backward.H_scomberoides.", "mrca.date.backward.Cynodon." ], "rows": 1000, "table": true, "tojson": true }, { "name": "laventa", "title": "Geochronology samples from the Honda Group in Colombia", "object": "laventa", "class": [ "data.frame" ], "fields": [ "age", "one_sigma", "sample", "unit", "elevation", "mineral", "comments" ], "rows": 87, "table": true, "tojson": true } ], "_help": [ { "page": "andes", "title": "Divergence-time estimation data for cis-trans-Andean pairs", "topics": [ "andes" ] }, { "page": "c_truncauchy", "title": "c_truncauchy: Estimate the c parameter for the truncated cauchy L distribution to be used in MCMCTree", "topics": [ "c_truncauchy" ] }, { "page": "concatNexus", "title": "concatNexus: Function for concatenation of nexus matrices both morphological and molecular", "topics": [ "concatNexus" ] }, { "page": "conflate", "title": "conflate: Calculate the conflation of multiple distributions pdfs, plot = TRUE, from, to, n, add = FALSE", "topics": [ "conflate" ] }, { "page": "crossplot", "title": "crossplot: Plot the mean/median and HPD interval bars for pairs of distributions", "topics": [ "crossplot" ] }, { "page": "cynodontidae.posterior", "title": "Posterior samples for the family Cynodontidae", "topics": [ "cynodontidae.posterior" ] }, { "page": "cynodontidae.prior", "title": "Prior samples for the family Cynodontidae", "topics": [ "cynodontidae.prior" ] }, { "page": "density_fun", "title": "density_fun: A way to represent distributions to be conflated", "topics": [ "density_fun" ] }, { "page": "fasta2nexus", "title": "fasta2nexus (deprecated): Function for converting molecular alignments from fasta to nexus format", "topics": [ "fasta2nexus" ] }, { "page": "findParams", "title": "Function for estimation of probability density function parameters through quadratic optimization", "topics": [ "findParams" ] }, { "page": "laventa", "title": "Geochronology samples from the Honda Group in Colombia", "topics": [ "laventa" ] }, { "page": "lognormalBeast", "title": 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"table2nexus" ] }, { "page": "tnt2newick", "title": "tnt2newick: Function for converting from TNT tree format to newick parenthetical format", "topics": [ "tnt2newick" ] }, { "page": "topoFreq", "title": "Frequency of topologies in a tree sample", "topics": [ "topoFreq" ] }, { "page": "xintercept", "title": "xintercept: Estimate the x-intercept of an empirical cdf", "topics": [ "xintercept" ] } ], "_pkglogo": "https://github.com/gaballench/tbea/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/gaballench/tbea/raw/HEAD/README.md", "_rundeps": [ "ape", "boot", "coda", "digest", "lattice", "nlme", "Rcpp", "Rfit" ], "_vignettes": [ { "source": "whyInitVals.Rmd", "filename": "whyInitVals.html", "title": "Why to use the mean of the quantiles as initial values in optim?", "author": "Gustavo A. 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