{ "_id": "6a1fd650b401979e734367c4", "Package": "DDD", "Type": "Package", "Title": "Diversity-Dependent Diversification", "Version": "5.2.5", "Authors@R": "c(\nperson(given = \"Rampal S.\",\nfamily = \"Etienne\",\nemail = \"r.s.etienne@rug.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2142-7612\")),\nperson(given = \"Bart\",\nfamily = \"Haegeman\",\nemail = \"bart.haegeman@sete.cnrs.fr\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2325-4727\")),\nperson(given = \"Hanno\",\nfamily = \"Hildenbrandt\",\nemail = \"h.hildenbrandt@rug.nl\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-6784-1037\")),\nperson(given = \"Giovanni\",\nfamily = \"Laudanno\",\nemail = \"glaudanno@gmail.com\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-2952-3345\"))\n)", "License": "GPL-3", "Encoding": "UTF-8", "Description": "Implements maximum likelihood and bootstrap methods based\non the diversity-dependent birth-death process to test whether\nspeciation or extinction are diversity-dependent, under various\nmodels including various types of key innovations. See Etienne\net al. 2012, Proc. Roy. Soc. B 279: 1300-1309,\n, Etienne & Haegeman 2012, Am. Nat.\n180: E75-E89, , Etienne et al. 2016. Meth.\nEcol. Evol. 7: 1092-1099, and\nLaudanno et al. 2021. Syst. Biol. 70: 389–407,\n. Also contains functions to\nsimulate the diversity-dependent process.", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "URL": "https://rsetienne.github.io/DDD/", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://rsetienne.r-universe.dev", "Date/Publication": "2026-05-04 13:47:55 UTC", "RemoteUrl": "https://github.com/rsetienne/ddd", "RemoteRef": "HEAD", "RemoteSha": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-03 06:57:58 UTC", "User": "root" }, "Author": "Rampal S. Etienne [aut, cre] (ORCID:\n),\nBart Haegeman [aut] (ORCID: ),\nHanno Hildenbrandt [ctb] (ORCID:\n),\nGiovanni Laudanno [ctb] (ORCID:\n)", "Maintainer": "Rampal S. Etienne ", "MD5sum": "5da06f8db5d8f3ea3541bb5265386e8a", "_user": "rsetienne", "_type": "src", "_file": "DDD_5.2.5.tar.gz", "_fileid": "16d700e01bf7e61dddd9bfcf99cb64d8669f564a2b399f191ca8f4d6e2bbf608", "_filesize": 306489, "_sha256": "16d700e01bf7e61dddd9bfcf99cb64d8669f564a2b399f191ca8f4d6e2bbf608", "_created": "2026-06-03T06:57:58.000Z", "_published": "2026-06-03T07:22:56.646Z", "_distro": "noble", "_jobs": [ { "job": 79239179083, "time": 209, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7377823513" }, { "job": 79239178774, "time": 211, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7377822891" }, { "job": 79239178833, "time": 213, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7377824464" }, { "job": 79239178797, "time": 193, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7377817587" }, { "job": 79239178808, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7377833235" }, { "job": 79239178767, "time": 447, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7377900864" }, { "job": 79239178764, "time": 164, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7377826114" }, { "job": 79239178762, "time": 489, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7377904550" }, { "job": 79238670229, "time": 214, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7377761678" }, { "job": 79239178746, "time": 1431, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79239178758, "time": 200, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7377819418" }, { "job": 79239178756, "time": 179, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7377813955" }, { "job": 79239178761, "time": 228, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7377827923" } ], "_buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rsetienne/ddd", "_commit": { "id": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "author": "Rampal S. Etienne ", "committer": "GitHub ", "message": "Merge pull request #63 from rsetienne/develop\n\nVersion number update", "time": 1777902475 }, "_maintainer": { "name": "Rampal S. Etienne", "email": "r.s.etienne@rug.nl", "login": "rsetienne", "description": "", "uuid": 14234521, "orcid": "0000-0003-2142-7612" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "version": ">= 1.0.10", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "BH", "version": ">= 1.81.0-1", "role": "LinkingTo" }, { "package": "deSolve", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "subplex", "role": "Imports" }, { "package": "DEoptim", "role": "Imports" }, { "package": "pso", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "SparseM", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.10", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "testit", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" } ], "_owner": "rsetienne", "_selfowned": true, "_usedby": 8, "_updates": [ { "week": "2025-48", "n": 1 }, { "week": "2026-17", "n": 1 }, { "week": "2026-19", "n": 1 } ], "_tags": [], "_stars": 4, "_contributors": [ { "user": "rsetienne", "count": 182, "uuid": 14234521 }, { "user": "neves-p", "count": 39, "uuid": 10762799 }, { "user": "thijsjanzen", "count": 10, "uuid": 19486664 }, { "user": "hhildenbrandt", "count": 9, "uuid": 38455490 }, { "user": "jeroen", "count": 2, "uuid": 216319 } ], "_userbio": { "uuid": 14234521, "type": "user", "name": "Rampal S. Etienne" }, "_downloads": { "count": 954, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DDD" }, "_mentions": 14, "_devurl": "https://github.com/rsetienne/ddd", "_pkgdown": "https://rsetienne.github.io/DDD/", "_searchresults": 91, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DDD.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rsetienne/ddd", "_realowner": "rsetienne", "_cranurl": true, "_releases": [ { "version": "0.2", "date": "2012-01-31" }, { "version": "0.3", "date": "2012-02-04" }, { "version": "0.4", "date": "2012-02-08" }, { "version": "1.1", "date": "2012-04-26" }, { "version": "1.2", "date": "2012-06-28" }, { "version": "1.3", "date": "2012-09-14" }, { "version": "1.4", "date": "2012-09-24" }, { "version": "1.5", "date": "2012-10-02" }, { "version": "1.7", "date": "2012-10-26" }, { "version": "1.8", "date": "2012-11-16" }, { "version": "1.9", "date": "2012-11-29" }, { "version": "1.10", "date": "2013-03-05" }, { "version": "1.11", "date": "2013-03-25" }, { "version": "2.0", "date": "2013-05-03" }, { "version": "2.1", "date": "2013-05-15" }, { "version": "2.2", "date": "2013-08-24" }, { "version": "2.3", "date": "2013-10-01" }, { "version": "2.4", "date": "2013-10-23" }, { "version": "2.5", "date": "2014-05-26" }, { "version": "2.6", "date": "2014-12-18" }, { "version": "2.7", "date": "2015-03-20" }, { "version": "3.0", "date": "2015-11-13" }, { "version": "3.1", "date": "2016-01-19" }, { "version": "3.2", "date": "2016-02-09" }, { "version": "3.3", "date": "2016-11-07" }, { "version": "3.4", "date": "2017-02-24" }, { "version": "3.5", "date": "2017-10-01" }, { "version": "3.6", "date": "2018-02-07" }, { "version": "3.7", "date": "2018-04-24" }, { "version": "3.8.1", "date": "2019-03-12" }, { "version": "3.9", "date": "2019-03-19" }, { "version": "4.0", "date": "2019-04-22" }, { "version": "4.1", "date": "2019-06-21" }, { "version": "4.2", "date": "2020-02-11" }, { "version": "4.3", "date": "2020-04-01" }, { "version": "4.4", "date": "2020-06-03" }, { "version": "4.4.1", "date": "2021-01-14" }, { "version": "5.0", "date": "2021-07-19" }, { "version": "5.2.1", "date": "2023-02-22" }, { "version": "5.2.2", "date": "2023-07-11" }, { "version": "5.2.4", "date": "2025-11-28" }, { "version": "5.2.5", "date": "2026-05-04" } ], "_exports": [ "bd_loglik", "bd_ML", "brts2phylo", "conv", "dd_KI_loglik", "dd_KI_ML", "dd_KI_sim", "dd_loglik", "dd_LR", "dd_ML", "dd_MS_loglik", "dd_MS_ML", "dd_MS_sim", "dd_sim", "dd_SR_loglik", "dd_SR_ML", "dd_SR_sim", "L2brts", "L2phylo", "optimizer", "phylo2L", "rng_respecting_sample", "roundn", "sample2", "simplex", "td_sim", "transform_pars", "untransform_pars" ], "_help": [ { "page": "bd_loglik", "title": "Loglikelihood for diversity-independent diversification model", "topics": [ "bd_loglik" ] }, { "page": "bd_ML", "title": "Maximization of the loglikelihood under the diversity-independent, possibly time-dependent diversification model", "topics": [ "bd_ML" ] }, { "page": "brts2phylo", "title": "Function to convert a set of branching times into a phylogeny with random topology This code is taken from the package TESS by Sebastian Hoehna, where the function is called tess.create.phylo", "topics": [ "brts2phylo" ] }, { "page": "conv", "title": "Function to do convolution of two vectors", "topics": [ "conv" ] }, { "page": "dd_KI_loglik", "title": "Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d", "topics": [ "dd_KI_loglik" ] }, { "page": "dd_KI_ML", "title": "Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics", "topics": [ "dd_KI_ML" ] }, { "page": "dd_KI_sim", "title": "Function to simulate a key innovation in macro-evolution with the innovative clade decoupling from the diversity-dependent diversification dynamics of the main clade", "topics": [ "dd_KI_sim" ] }, { "page": "dd_loglik", "title": "Loglikelihood for diversity-dependent diversification models", "topics": [ "dd_loglik" ] }, { "page": "dd_LR", "title": "Bootstrap likelihood ratio test of diversity-dependent diversification model", "topics": [ "dd_LR" ] }, { "page": "dd_ML", "title": "Maximization of the loglikelihood under a diversity-dependent diversification model", "topics": [ "dd_ML" ] }, { "page": "dd_MS_loglik", "title": "Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d", "topics": [ "dd_MS_loglik" ] }, { "page": "dd_MS_ML", "title": "Maximization of the loglikelihood under a diversity-dependent diversification model with decoupling of a subclade's diversication dynamics from the main clade's dynamics", "topics": [ "dd_MS_ML" ] }, { "page": "dd_MS_sim", "title": "Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification", "topics": [ "dd_MS_sim" ] }, { "page": "dd_multiple_KI_loglik", "title": "Loglikelihood for diversity-dependent diversification models with multiple decoupling (rate shift) events", "topics": [ "dd_multiple_KI_loglik" ] }, { "page": "dd_sim", "title": "Function to simulate the diversity-dependent diversification process", "topics": [ "dd_sim" ] }, { "page": "dd_SR_loglik", "title": "Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift", "topics": [ "dd_SR_loglik" ] }, { "page": "dd_SR_ML", "title": "Maximization of the loglikelihood under a diversity-dependent diversification model with a shift in the parameters", "topics": [ "dd_SR_ML" ] }, { "page": "dd_SR_sim", "title": "Function to simulate the diversity-dependent diversification process with a shift in one or more of the parameters", "topics": [ "dd_SR_sim" ] }, { "page": "L2brts", "title": "Function to convert a table with speciation and extinction events to a set of branching times", "topics": [ "L2brts" ] }, { "page": "L2phylo", "title": "Function to convert a table with speciation and extinction events to a phylogeny", "topics": [ "L2phylo" ] }, { "page": "optimizer", "title": "Carries out optimization (finding a maximum)", "topics": [ "optimizer" ] }, { "page": "phylo2L", "title": "Function to convert phylogeny to a table with speciation and extinction events", "topics": [ "phylo2L" ] }, { "page": "rng_respecting_sample", "title": "Sampling in which zero probabilities are removed", "topics": [ "rng_respecting_sample" ] }, { "page": "roundn", "title": "Rounds up in the usual manner", "topics": [ "roundn" ] }, { "page": "sample2", "title": "Takes samples in the usual manner", "topics": [ "sample2" ] }, { "page": "simplex", "title": "Carries out optimization using a simplex algorithm (finding a minimum)", "topics": [ "simplex" ] }, { "page": "td_sim", "title": "Simulation of a diversity-dependent-like time-dependent process", "topics": [ "td_sim" ] }, { "page": "transform_pars", "title": "Transforming parameters from -Inf to Inf into parameters from -1 to 1", "topics": [ "transform_pars" ] }, { "page": "untransform_pars", "title": "Untransforming parameters from -1 to 1 into parameters from -Inf to Inf.", "topics": [ "untransform_pars" ] } ], "_readme": "https://github.com/rsetienne/ddd/raw/HEAD/README.md", "_rundeps": [ "ape", "BH", "cli", "clusterGeneration", "coda", "codetools", "combinat", "cpp11", "DEoptim", "deSolve", "digest", "doParallel", "expm", "fastmatch", "foreach", "generics", "glue", "igraph", "iterators", "lattice", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "mnormt", "nlme", "numDeriv", "optimParallel", "phangorn", "phytools", "pkgconfig", "pso", "quadprog", "Rcpp", "RcppEigen", "rlang", "scatterplot3d", "SparseM", "subplex", "vctrs" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 7.719463875744306, "_indexed": true, "_nocasepkg": "ddd", "_universes": [ "rsetienne" ], "_binaries": [ { "r": "4.6.0", "os": "wasm", "version": "5.2.5", "date": "2026-05-22T17:18:04.000Z", "arch": "emscripten", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "656cc44229adfc8c394ba04e29b56439fcd36f8fdc1e605df458dd699e218a32", "status": "success", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/25326852014" }, { "r": "4.7.0", "os": "linux", "version": "5.2.5", "date": "2026-06-03T07:00:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "4a939b8deb5aba26acc0950aa53a7ce9c3782e9b2736dc0c2dd6c2723a364da8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.7.0", "os": "linux", "version": "5.2.5", "date": "2026-06-03T07:00:57.000Z", "distro": "noble", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "417d46174ef98729329f2924afabeb78a35d17a9b4f07057bec93c57fea6141e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.6.0", "os": "linux", "version": "5.2.5", "date": "2026-06-03T07:01:01.000Z", "distro": "noble", "arch": "aarch64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "519a3352e34494f47d090a87eaad7e6d76114ebc1d32c4e8ce63c0082d02b226", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.6.0", "os": "linux", "version": "5.2.5", "date": "2026-06-03T07:00:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "3a211374ca371e2940a4794808900d7592096d6bc1ae7342bcf477522f9a2155", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.5.3", "os": "mac", "version": "5.2.5", "date": "2026-06-03T07:01:44.000Z", "arch": "aarch64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "5584c016d133a455935315b50eda2988beafed34b7ef249df4d58322e3b61993", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.5.3", "os": "mac", "version": "5.2.5", "date": "2026-06-03T07:03:38.000Z", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "7eb5d8aad952a0f962c05beae14511cc661761bf020d9230cd42804058dd58e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.6.0", "os": "mac", "version": "5.2.5", "date": "2026-06-03T07:01:20.000Z", "arch": "aarch64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "084ab3d466089e9e37b41141e4f23c39da84bdc76638594bc6d4b17db4ad828f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.6.0", "os": "mac", "version": "5.2.5", "date": "2026-06-03T07:03:44.000Z", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "d9878303c05518856807964a0f7aa5cfc62429c5dedd303efee70515dea31b17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.7.0", "os": "win", "version": "5.2.5", "date": "2026-06-03T07:00:02.000Z", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "8a79a3715011cfd6982fd7474c8af3c60767b395efdf2d45434f6da8f6a142bd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.5.3", "os": "win", "version": "5.2.5", "date": "2026-06-03T07:00:05.000Z", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "a1e2a8b3cd179ace13de2425062f6014764a754f8898c04cf4b5272c1e73c589", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" }, { "r": "4.6.0", "os": "win", "version": "5.2.5", "date": "2026-06-03T06:59:54.000Z", "arch": "x86_64", "commit": "e52af505d79bc35f8e3c1d9447b6783252a18d20", "fileid": "6eb8aa365c38d16c96fc77821e7731beb83c73c9b31517a5f3fee062fad600a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/26868784660" } ] }