{ "_id": "6a4795712f27a93436c0e2e2", "Package": "PBD", "Type": "Package", "Title": "Protracted Birth-Death Model of Diversification", "Version": "1.5", "Date": "2017-5-10", "Author": "Rampal S. Etienne", "Maintainer": "Rampal S. Etienne ", "Description": "Conducts maximum likelihood analysis and simulation of the\nprotracted birth-death model of diversification. See Etienne,\nR.S. & J. Rosindell 2012 ; Lambert,\nA., H. Morlon & R.S. Etienne 2014,\n; Etienne, R.S., H. Morlon & A.\nLambert 2014, .", "License": "GPL-2", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.0", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://rsetienne.r-universe.dev", "Date/Publication": "2025-02-10 13:16:54 UTC", "RemoteUrl": "https://github.com/rsetienne/pbd", "RemoteRef": "HEAD", "RemoteSha": "927c8f48112048827d87bcf58f361e0f6aea38fb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 05:31:01 UTC", "User": "root" }, "_user": "rsetienne", "_type": "src", "_file": "PBD_1.5.tar.gz", "_fileid": "https://r2.ropensci.org/e4655a46964380b7ec38ee4ec88b00b2579b185f88a383f79ecb7f401209898a", "_filesize": 511176, "_sha256": "e4655a46964380b7ec38ee4ec88b00b2579b185f88a383f79ecb7f401209898a", "_expires": "2026-10-11T10:56:48.000Z", "_created": "2026-07-03T05:31:01.000Z", "_published": "2026-07-03T10:56:49.200Z", "_jobs": [ { "job": 84985232451, "time": 165, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8058557178" }, { "job": 84985232877, "time": 152, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8058554292" }, { "job": 84985232701, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8058547460" }, { "job": 84985232447, "time": 93, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8058541969" }, { "job": 84985232377, "time": 199, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8058521689" }, { "job": 84985232978, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8058554935" }, { "job": 84985232529, "time": 94, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8058542359" }, { "job": 84985232791, "time": 104, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8058544233" }, { "job": 84985232592, "time": 104, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8058544069" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885", "_status": "success", "_upstream": "https://github.com/rsetienne/pbd", "_commit": { "id": "927c8f48112048827d87bcf58f361e0f6aea38fb", "author": "rsetienne ", "committer": "rsetienne ", "message": "Folder move\n", "time": 1739193414 }, "_maintainer": { "name": "Rampal S. Etienne", "email": "r.s.etienne@rug.nl", "login": "rsetienne", "description": "", "uuid": 14234521 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "deSolve", "role": "Imports" }, { "package": "ade4", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "DDD", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testit", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "rsetienne", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "rsetienne", "count": 35, "uuid": 14234521 }, { "user": "richelbilderbeek", "count": 10, "uuid": 2098230 }, { "user": "j-damhuis", "count": 4, "uuid": 38530704 } ], "_userbio": { "uuid": 14234521, "type": "user", "name": "Rampal S. Etienne", "followers": 25 }, "_downloads": { "count": 305, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PBD" }, "_mentions": 9, "_devurl": "https://github.com/rsetienne/pbd", "_searchresults": 55, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PBD.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rsetienne/pbd", "_realowner": "rsetienne", "_cranurl": true, "_releases": [ { "version": "0.8", "date": "2014-04-01" }, { "version": "0.9", "date": "2014-04-17" }, { "version": "1.0", "date": "2014-05-26" }, { "version": "1.1", "date": "2015-09-29" }, { "version": "1.2", "date": "2016-03-04" }, { "version": "1.3", "date": "2017-04-29" }, { "version": "1.4", "date": "2017-05-04" } ], "_exports": [ "pbd_bootstrap", "pbd_brts_density", "pbd_durspec_cumdensity", "pbd_durspec_density", "pbd_durspec_mean", "pbd_durspec_mode", "pbd_durspec_moment", "pbd_durspec_quantile", "pbd_durspec_var", "pbd_loglik", "pbd_LR", "pbd_mean_durspec", "pbd_mean_durspecs", "pbd_ML", "pbd_numspec_mean", "pbd_numspec_median", "pbd_numspec_quantile", "pbd_sim", "pbd_sim_checked", "pbd_sim_cpp" ], "_help": [ { "page": "PBD-package", "title": "Protracted Birth-Death Model of Diversification", "topics": [ "PBD-package", "PBD" ] }, { "page": "pbd_bootstrap", "title": "Bootstrap analysis under protracted birth-death model of diversification", "topics": [ "pbd_bootstrap" ] }, { "page": "pbd_brts_density", "title": "Node depth probbaility density for protracted birth-death model of diversification", "topics": [ "pbd_brts_density" ] }, { "page": "pbd_durspec_cumdensity", "title": "Cumulative density of duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_cumdensity" ] }, { "page": "pbd_durspec_density", "title": "Probability density for duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_density" ] }, { "page": "pbd_durspec_mean", "title": "Mean duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_mean" ] }, { "page": "pbd_durspec_mean_impl", "title": "Actual calculation of the mean duration of speciation (equations 19 and 20 of reference article) assuming all inputs are correct", "topics": [ "pbd_durspec_mean_impl" ] }, { "page": "pbd_durspec_mode", "title": "mode of the duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_mode" ] }, { "page": "pbd_durspec_moment", "title": "Moments of duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_moment" ] }, { "page": "pbd_durspec_quantile", "title": "Quantiles of duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_quantile" ] }, { "page": "pbd_durspec_var", "title": "Variance in duration of speciation under protracted birth-death model of diversification", "topics": [ "pbd_durspec_var" ] }, { "page": "pbd_loglik", "title": "Loglikelihood for protracted birth-death model of diversification", "topics": [ "pbd_loglik" ] }, { "page": "pbd_LR", "title": "Bootstrap likelihood ratio test of protracted birth-death model of diversification", "topics": [ "pbd_LR" ] }, { "page": "pbd_mean_durspec", "title": "Calculate the mean duration of speciation (equations 19 and 20 of reference article), non-vectorized", "topics": [ "pbd_mean_durspec" ] }, { "page": "pbd_mean_durspecs", "title": "Calculate the mean durations of speciation (equations 19 and 20 of reference article)", "topics": [ "pbd_mean_durspecs" ] }, { "page": "pbd_ML", "title": "Maximization of loglikelihood under protracted birth-death model of diversification", "topics": [ "pbd_ML" ] }, { "page": "pbd_numspec_mean", "title": "Mean number of species under protracted birth-death model of diversification", "topics": [ "pbd_numspec_mean" ] }, { "page": "pbd_numspec_median", "title": "Median number of species under protracted birth-death model of diversification", "topics": [ "pbd_numspec_median" ] }, { "page": "pbd_numspec_quantile", "title": "Number of species for a given quantile under protracted birth-death model of diversification", "topics": [ "pbd_numspec_quantile" ] }, { "page": "pbd_sim", "title": "Function to simulate the protracted speciation process", "topics": [ "pbd_sim" ] }, { "page": "pbd_sim_checked", "title": "Checked and safer version of PBD::pbd_sim", "topics": [ "pbd_sim_checked" ] }, { "page": "pbd_sim_cpp", "title": "Function to simulate the approximate protracted speciation process", "topics": [ "pbd_sim_cpp" ] } ], "_readme": "https://github.com/rsetienne/pbd/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "BH", "cli", "clusterGeneration", "coda", "codetools", "combinat", "cpp11", "DDD", "DEoptim", "deSolve", "digest", "doParallel", "expm", "fastmatch", "foreach", "generics", "glue", "igraph", "iterators", "lattice", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "mnormt", "nlme", "numDeriv", "optimParallel", "phangorn", "phytools", "pixmap", "pkgconfig", "pso", "quadprog", "Rcpp", "RcppArmadillo", "RcppEigen", "rlang", "scatterplot3d", "sp", "SparseM", "subplex", "testit", "vctrs" ], "_vignettes": [ { "source": "PBD_ML_demo.Rmd", "filename": "PBD_ML_demo.html", "title": "pbd_ML demo", "author": "Richel Bilderbeek & Rampal S. Etienne", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-02-10 13:16:54", "modified": "2025-02-10 13:16:54", "commits": 1 } ], "_score": 5.995635194597551, "_indexed": true, "_nocasepkg": "pbd", "_universes": [ "rsetienne" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5", "date": "2026-07-03T05:33:39.000Z", "distro": "resolute", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/1bf864d80f8f787f34a84a3b6f6a00e1c40be69a62a17482285bc05372e22f8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.6.1", "os": "linux", "version": "1.5", "date": "2026-07-03T05:33:26.000Z", "distro": "resolute", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/85196afd3b28356fb6fbb1235055c79c57012ef8b7ab4d43059fa9e89d868edd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.5.3", "os": "mac", "version": "1.5", "date": "2026-07-03T05:32:56.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/34d3dfc03014da65541a9ee541e910b9002fd532f367c6bb2328357bb9bdbe86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.6.1", "os": "mac", "version": "1.5", "date": "2026-07-03T05:32:34.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/d6558bb14235ef568f0a5682521f4aa3620b028935be17a737103edff75e1404", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.6.0", "os": "wasm", "version": "1.5", "date": "2026-07-03T05:33:51.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/b50c14bec0db12a418a13122918ab434ba4275c7f3231d9f848b06c51e935ae9", "status": "success", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.7.0", "os": "win", "version": "1.5", "date": "2026-07-03T05:32:21.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/149232877ff66ede1253c87d5a69750ab553fc19685687e7ae06b6d3d6202c05", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.5.3", "os": "win", "version": "1.5", "date": "2026-07-03T05:32:31.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/5e9f16577fdc7c83905b72e4522cbc5204b1b0661904bc2011411fe911943d60", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" }, { "r": "4.6.1", "os": "win", "version": "1.5", "date": "2026-07-03T05:32:31.000Z", "commit": "927c8f48112048827d87bcf58f361e0f6aea38fb", "fileid": "https://r2.ropensci.org/f01e0a23952bc8d8a5f7d16ea632fd4eb7f9becb5a6cb51b4275f92480a2d35c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640478885" } ] }