{ "_id": "6a3199f43efcd9bda436de71", "Package": "treats", "Title": "Trees and Traits Simulations", "Authors@R": "c(person(\"Thomas\", \"Guillerme\", role = c(\"aut\", \"cre\", \"cph\"), email = \"guillert@tcd.ie\", comment = c(ORCID = \"0000-0003-4325-1275\")))", "Version": "1.1.6", "Date": "2025-05-15", "Description": "A modular package for simulating phylogenetic trees and\nspecies traits jointly. Trees can be simulated using modular\nbirth-death parameters (e.g. changing starting parameters or\nalgorithm rules). Traits can be simulated in any way designed\nby the user. The growth of the tree and the traits can\ninfluence each other through modifiers objects providing rules\nfor affecting each other. Finally, events can be created to\nmodify both the tree and the traits under specific conditions (\nGuillerme, 2024 ).", "NeedsCompilation": "no", "License": "GPL-3", "RoxygenNote": "7.3.2", "URL": "https://github.com/TGuillerme/treats", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nlibgmp3-dev make texlive libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev libx11-dev zlib1g-dev", "Repository": "https://tguillerme.r-universe.dev", "Date/Publication": "2025-05-15 10:47:28 UTC", "RemoteUrl": "https://github.com/tguillerme/treats", "RemoteRef": "HEAD", "RemoteSha": "612c33a3b12047b58f21da99fb411ab975853256", "Packaged": { "Date": "2026-06-16 18:40:46 UTC", "User": "root" }, "Author": "Thomas Guillerme [aut, cre, cph] (ORCID:\n)", "Maintainer": "Thomas Guillerme ", "MD5sum": "558f654c608361878c059c690c225e65", "_user": "tguillerme", "_type": "src", "_file": "treats_1.1.6.tar.gz", "_fileid": "6da2b359dfcafe2cb0df1aafb35722e8111584dea14cd6b277cd2792faddc0f6", "_filesize": 11343899, "_sha256": "6da2b359dfcafe2cb0df1aafb35722e8111584dea14cd6b277cd2792faddc0f6", "_created": "2026-06-16T18:40:46.000Z", "_published": "2026-06-16T18:46:12.579Z", "_distro": "noble", "_jobs": [ { "job": 81736914546, "time": 237, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7676445195" }, { "job": 81736914476, "time": 271, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7676456480" }, { "job": 81736914511, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7676408630" }, { "job": 81736914540, "time": 155, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7676411095" }, { "job": 81735982219, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7676350266" }, { "job": 81736914584, "time": 197, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7676428009" }, { "job": 81736914544, "time": 174, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7676421338" }, { "job": 81736914694, "time": 165, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7676417114" }, { "job": 81736914533, "time": 170, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7676419210" } ], "_buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/tguillerme/treats", "_commit": { "id": "612c33a3b12047b58f21da99fb411ab975853256", "author": "Thomas Guillerme ", "committer": "GitHub ", "message": "Update test-coverage.yaml", "time": 1747306048 }, "_maintainer": { "name": "Thomas Guillerme", "email": "guillert@tcd.ie", "login": "tguillerme", "mastodon": "@TGuillerme@mastodon.social", "description": "Macroevolution, macroecology, phylogenomics, palaeontology, beer taxonomy and unplanned stuff.", "uuid": 3206086, "orcid": "0000-0003-4325-1275" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "dispRity", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "geiger", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rgl", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "tguillerme", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "tguillerme", "count": 675, "uuid": 3206086 }, { "user": "lrombaut", "count": 1, "uuid": 125313530 } ], "_userbio": { "uuid": 3206086, "type": "user", "name": "Thomas Guillerme", "followers": 98, "description": "Macroevolution, macroecology, phylogenomics, palaeontology, beer taxonomy and unplanned stuff." }, "_downloads": { "count": 616, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treats" }, "_devurl": "https://github.com/tguillerme/treats", "_searchresults": 33, "_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/readme.html", "extra/readme.md", "extra/treats.html", "manual.pdf" ], "_homeurl": "https://github.com/tguillerme/treats", "_realowner": "tguillerme", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2023-11-24" }, { "version": "1.1", "date": "2024-11-14" }, { "version": "1.1.6", "date": "2025-05-15" } ], "_exports": [ "age.condition", "bd.params.update", "BM.process", "branch.length", "branch.length.trait", "crude.bd.est", "discrete.process", "dispRitreats", "drop.fossils", "drop.livings", "drop.singles", "drop.things", "drop.tip.treats", "events.condition", "events.modification", "founding.event", "keep.tip.treats", "link.traits", "make.bd.params", "make.events", "make.modifiers", "make.traits", "make.treats", "map.traits", "modifiers", "modifiers.update", "multi.peak.process", "no.process", "OU.process", "parent.traits", "plot.treats", "print.treats", "random.extinction", "repulsion.process", "selection", "speciation", "speciation.trait", "taxa.condition", "trait.condition", "trait.extinction", "trait.process", "traits.update", "transition.matrix", "treats" ], "_help": [ { "page": "crude.bd.est", "title": "Crudely estimates extinction and speciation", "topics": [ "crude.bd.est" ] }, { "page": "dispRitreats", "title": "dispRity interface for treats objects", "topics": [ "dispRitreats" ] }, { "page": "drop.things", "title": "Drop things from a treats object", "topics": [ "drop.fossils", "drop.livings", "drop.singles", "drop.things" ] }, { "page": "drop.tip.treats", "title": "drop.tip.treats", "topics": [ "drop.tip.treats", "keep.tip.treats" ] }, { "page": "events.conditions", "title": "events.conditions", "topics": [ "age.condition", "events.condition", "events.conditions", "taxa.condition", "trait.condition" ] }, { "page": "events.modifications", "title": "Events modifications", "topics": [ "bd.params.update", "events.modification", "events.modifications", "founding.event", "modifiers.update", "random.extinction", "trait.extinction", "traits.update" ] }, { "page": "link.traits", "title": "link.traits", "topics": [ "link.traits" ] }, { "page": "make.bd.params", "title": "Make birth death parameters", "topics": [ "make.bd.params" ] }, { "page": "make.events", "title": "make.events", "topics": [ "make.events" ] }, { "page": "make.modifiers", "title": "make.modifiers", "topics": [ "make.modifiers" ] }, { "page": "make.traits", "title": "make.traits", "topics": [ "make.traits" ] }, { "page": "make.treats", "title": "Make a treats object", "topics": [ "make.treats" ] }, { "page": "map.traits", "title": "Maps a trait on a tree", "topics": [ "map.traits" ] }, { "page": "modifiers", "title": "Modifiers", "topics": [ "branch.length", "branch.length.trait", "modifiers", "selection", "speciation", "speciation.trait" ] }, { "page": "parent.traits", "title": "Get parent traits", "topics": [ "parent.traits" ] }, { "page": "plot.treats", "title": "Plot treats objects", "topics": [ "plot.treats" ] }, { "page": "print.treats", "title": "Prints a 'treats' object.", "topics": [ "print.treats" ] }, { "page": "trait.process", "title": "Trait processes", "topics": [ "BM.process", "discrete.process", "multi.peak.process", "no.process", "OU.process", "repulsion.process", "trait.process" ] }, { "page": "transition.matrix", "title": "Makes a transition matrix", "topics": [ "transition.matrix" ] }, { "page": "treats", "title": "Diversity and disparity simulator", "topics": [ "treats" ] } ], "_readme": "https://github.com/tguillerme/treats/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "ape", "base64enc", "bslib", "cachem", "castor", "Claddis", "cli", "clipr", "cluster", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "cpp11", "DEoptim", "deSolve", "digest", "dispRity", "doParallel", "ellipse", "evaluate", "expm", "farver", "fastmap", "fastmatch", "fontawesome", "foreach", "fs", "future", "future.apply", "geiger", "generics", "geometry", "geoscale", "GET", "ggplot2", "globals", "glue", "gmp", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "linprog", "listenv", "lpSolve", "magic", "magrittr", "maps", "MASS", "Matrix", "memoise", "mgcv", "mime", "mnormt", "multicool", "mvtnorm", "naturalsort", "ncbit", "nlme", "numDeriv", "optimParallel", "parallelly", "partitions", "pbapply", "permute", "phangorn", "phyclust", "phylolm", "phytools", "pixmap", "pkgconfig", "polynom", "quadprog", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppProgress", "Rdpack", "rgl", "rlang", "rmarkdown", "RSpectra", "S7", "sass", "scales", "scatterplot3d", "sets", "sp", "strap", "subplex", "tinytex", "vctrs", "vegan", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_score": 3.6946051989335684, "_indexed": true, "_nocasepkg": "treats", "_universes": [ "tguillerme" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.6", "date": "2026-06-16T18:44:13.000Z", "distro": "noble", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "5ca172c1680ec289ecb39874cae9140be5dd6fa0001cddf9b0c69782cfa79e4d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.6.0", "os": "linux", "version": "1.1.6", "date": "2026-06-16T18:44:26.000Z", "distro": "noble", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "2ffa14c7c1a00937d38009f7971b466a5153cd9ccf9c54806b99acba5203d68d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.5.3", "os": "mac", "version": "1.1.6", "date": "2026-06-16T18:42:47.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "563e8c49382438444e7af56137dc6eac2d543349475dbc0c65b7e338e3bca6b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.6.0", "os": "mac", "version": "1.1.6", "date": "2026-06-16T18:42:46.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "3080eef2028a21ab79babf5785cbc6630795451cbea16edff085d137c3d8f4b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.6", "date": "2026-06-16T18:44:30.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "34897a878c368b2fee77ee28be9e490f372d1f6c709101a2004696bbbe459150", "status": "success", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.7.0", "os": "win", "version": "1.1.6", "date": "2026-06-16T18:42:43.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "92a9f439543d50d376d19b78e8acdad6298a59da6a46c1d8948fe36c719191f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.5.3", "os": "win", "version": "1.1.6", "date": "2026-06-16T18:42:30.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "5b1988faaacac8b1826a7f7ce5cd73f86f77e9b783a6eacea15992bd5cc9929d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" }, { "r": "4.6.0", "os": "win", "version": "1.1.6", "date": "2026-06-16T18:42:30.000Z", "commit": "612c33a3b12047b58f21da99fb411ab975853256", "fileid": "cdbb19c0de1efbaa215e01ab9942903f0736ced4167140817949e68a36eafc26", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tguillerme/actions/runs/27639622250" } ] }