{ "_id": "6a27a9d324555f66ed533e23", "Package": "paleobuddy", "Title": "Simulating Diversification Dynamics", "Version": "1.1.0", "Authors@R": "c(\nperson(given = \"Bruno\",\nfamily = \"do Rosario Petrucci\",\nrole = c(\"aut\", \"cre\"),\nemail = \"petrucci@iastate.edu\",\ncomment = c(ORCID = \"0000-0001-6334-8483\")),\nperson(given = \"Matheus\",\nfamily = \"Januario\",\nrole = \"aut\",\nemail = \"januarioml.eco@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6480-7095\")),\nperson(given = \"Tiago\",\nfamily = \"Quental\",\nrole = \"aut\",\nemail = \"tbquental@usp.br\",\ncomment = c(ORCID = \"0000-0002-4832-9468\")))", "Description": "Simulation of species diversification, fossil records, and\nphylogenies. While the literature on species birth-death\nsimulators is extensive, including important software like\n'paleotree' and 'APE', we concluded there were interesting gaps\nto be filled regarding possible diversification scenarios. Here\nwe strove for flexibility over focus, implementing a large\narray of regimens for users to experiment with and combine. In\nthis way, 'paleobuddy' can be used in complement to other\nsimulators as a flexible jack of all trades, or, in the case of\nscenarios implemented only here, can allow for robust and easy\nsimulations for novel situations. Environmental data modified\nfrom that in 'RPANDA': Morlon H. et al (2016)\n.", "URL": "https://github.com/brpetrucci/paleobuddy", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "BugReports": "https://github.com/brpetrucci/paleobuddy/issues", "Repository": "https://brpetrucci.r-universe.dev", "Date/Publication": "2025-02-05 17:53:30 UTC", "RemoteUrl": "https://github.com/brpetrucci/paleobuddy", "RemoteRef": "HEAD", "RemoteSha": "47e7730ca37cd61d638c6a18dee094ab63d0cb69", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-08 08:23:51 UTC", "User": "root" }, "Author": "Bruno do Rosario Petrucci [aut, cre] (ORCID:\n),\nMatheus Januario [aut] (ORCID: ),\nTiago Quental [aut] (ORCID: )", "Maintainer": "Bruno do Rosario Petrucci ", "MD5sum": "6063ef6974aae8b068dcb9e18ff0d3e2", "_user": "brpetrucci", "_type": "src", "_file": "paleobuddy_1.1.0.tar.gz", "_fileid": "4d37b3b9767010a7ff9571184c148fa6f3c67b6a997664a89a3df73fda933b9e", "_filesize": 2594672, "_sha256": "4d37b3b9767010a7ff9571184c148fa6f3c67b6a997664a89a3df73fda933b9e", "_created": "2026-06-08T08:23:51.000Z", "_published": "2026-06-09T05:51:15.708Z", "_distro": "noble", "_jobs": [ { "job": 80256892851, "time": 130, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7474984428" }, { "job": 80256892726, "time": 99, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7474974864" }, { "job": 80256892681, "time": 159, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7474987757" }, { "job": 80256892538, "time": 171, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7474989860" }, { "job": 80256892347, "time": 238, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7474942597" }, { "job": 80256892576, "time": 95, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7474973976" }, { "job": 80256892536, "time": 208, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7475008596" }, { "job": 80256892552, "time": 103, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7474976297" }, { "job": 80256892349, "time": 89, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7499526405" } ], "_buildurl": "https://github.com/r-universe/brpetrucci/actions/runs/27124933522", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/brpetrucci/paleobuddy", "_commit": { "id": "47e7730ca37cd61d638c6a18dee094ab63d0cb69", "author": "brpetrucci ", "committer": "brpetrucci ", "message": "Set an example in sample.clade to not run due to CRAN rejection. Changed some internal function names to avoid confusing roxygen2. Added _PACKAGE to paleobuddy.R. Resubmitted to CRAN.\n", "time": 1738778010 }, "_maintainer": { "name": "Bruno do Rosario Petrucci", "email": "petrucci@iastate.edu", "login": "brpetrucci", "uuid": 33266986, "orcid": "0000-0001-6334-8483" }, "_registered": true, "_dependencies": [ { "package": "methods", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "fitdistrplus", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "brpetrucci", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "evolution", "macroevolution", "paleobiology", "paleontology", "phylogenetics" ], "_stars": 9, "_contributors": [ { "user": "brpetrucci", "count": 343, "uuid": 33266986 }, { "user": "mjanuario", "count": 81, "uuid": 14234924 } ], "_userbio": { "uuid": 33266986, "type": "user", "name": "Bruno do Rosario Petrucci", "description": "PhD student at the Heath lab on Iowa State University. I'm interested in mathematical modelling of diversification dynamics, particularly mass extinction events" }, "_downloads": { "count": 172, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/paleobuddy" }, "_devurl": "https://github.com/brpetrucci/paleobuddy", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/paleobuddy.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/brpetrucci/paleobuddy", "_realowner": "brpetrucci", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-12-21" }, { "version": "1.1.0", "date": "2025-02-05" } ], "_exports": [ "bd.sim", "bd.sim.traits", "bin.occurrences", "binner", "draw.sim", "find.lineages", "is.sim", "make.phylo", "make.rate", "phylo.to.sim", "rexp.var", "sample.clade", "sample.clade.traits", "sim.counts", "traits.summary", "var.rate.div" ], "_datasets": [ { "name": "co2", "title": "Jurassic CO2 data", "object": "co2", "class": [ "data.frame" ], "fields": [ "t", "co2" ], "rows": 53, "table": true, "tojson": true }, { "name": "temp", "title": "Cenozoic temperature data", "object": "temp", "class": [ "data.frame" ], "fields": [ "t", "temperature" ], "rows": 17632, "table": true, "tojson": true } ], "_help": [ { "page": "bd.sim", "title": "General rate Birth-Death simulation", "topics": [ "bd.sim" ] }, { "page": "bd.sim.traits", "title": "MuSSE simulation", "topics": [ "bd.sim.traits" ] }, { "page": "bin.occurrences", "title": "Bin true occurrences into geologic intervals", "topics": [ "bin.occurrences" ] }, { "page": "binner", "title": "Bin occurrences in geologic intervals", "topics": [ "binner" ] }, { "page": "co2", "title": "Jurassic CO2 data", "topics": [ "co2" ] }, { "page": "draw.sim", "title": "Draw a sim object", "topics": [ "draw.sim" ] }, { "page": "find.lineages", "title": "Separate a paleobuddy simulation into monophyletic clades", "topics": [ "find.lineages" ] }, { "page": "make.phylo", "title": "Phylogeny generating", "topics": [ "make.phylo" ] }, { "page": "make.rate", "title": "Create a flexible rate for birth-death or sampling simulations", "topics": [ "make.rate" ] }, { "page": "paleobuddy", "title": "paleobuddy: Simulating diversification dynamics", "topics": [ "paleobuddy-package", "paleobuddy" ] }, { "page": "phylo.to.sim", "title": "Converting a phylogeny in a paleobuddy object", "topics": [ "phylo.to.sim" ] }, { "page": "rexp.var", "title": "General rate exponential and Weibull waiting times", "topics": [ "rexp.var" ] }, { "page": "sample.clade", "title": "General rate fossil sampling", "topics": [ "sample.clade" ] }, { "page": "sample.clade.traits", "title": "Trait-dependent fossil sampling", "topics": [ "sample.clade.traits" ] }, { "page": "sim", "title": "Details, generics, and methods for the 'sim' class", "topics": [ "head.sim", "is.sim", "plot.sim", "print.sim", "sim", "sim.counts", "summary.sim", "tail.sim" ] }, { "page": "temp", "title": "Cenozoic temperature data", "topics": [ "temp" ] }, { "page": "traits.summary", "title": "Summarizing trait data", "topics": [ "traits.summary" ] }, { "page": "var.rate.div", "title": "Expected diversity for general exponential rates", "topics": [ "var.rate.div" ] } ], "_readme": "https://github.com/brpetrucci/paleobuddy/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "overview.Rmd", "filename": "overview.html", "title": "Paleobuddy overview", "author": "Bruno do Rosario Petrucci", "engine": "knitr::rmarkdown", "headings": [ "Constant rate birth-death", "Time-dependent speciation and extinction", "paleobuddy's flexibility", "State-dependent speciation, extinction, and fossil sampling", "Conclusion" ], "created": "2020-07-17 16:42:15", "modified": "2023-10-17 14:50:48", "commits": 21 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": 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