{ "_id": "69db419bc5259ad4cd85b4ed", "Package": "babette", "Title": "Control 'BEAST2'", "Version": "2.3.5", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"rjcbilderbeek@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Joëlle\", \"Barido-Sottani\", role = \"rev\", comment = \"Joëlle reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209\"),\nperson(\"David\", \"Winter\", role = \"rev\", comment = \"David reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209\"),\nperson(\"Jason\", \"Griffiths\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1667-8233\")),\nperson(\"Olivier\", \"Roy\", role = \"ctb\"),\nperson(\"Tanmay\", \"Dimri\", role = \"ctb\"),\nperson(\"Giovanni\", \"Laudanno\", email = \"glaudanno@gmail.com\", role = \"ctb\"))", "Description": "'BEAST2' () is a widely used\nBayesian phylogenetic tool, that uses DNA/RNA/protein data and\nmany model priors to create a posterior of jointly estimated\nphylogenies and parameters. 'BEAST2' is commonly accompanied by\n'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an\nalternative workflow of using all these tools separately. This\nallows doing complex Bayesian phylogenetics easily and\nreproducibly from 'R'.", "License": "GPL-3", "RoxygenNote": "7.3.3.9000", "VignetteBuilder": "knitr", "URL": "https://docs.ropensci.org/babette/ (website),\nhttps://github.com/ropensci/babette", "BugReports": "https://github.com/ropensci/babette/issues", "Language": "en-US", "Encoding": "UTF-8", "SystemRequirements": "BEAST2 (https://www.beast2.org/)", "Config/pak/sysreqs": "libglpk-dev make default-jdk libicu-dev libxml2-dev\nlibx11-dev zlib1g-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-03-13 06:22:44 UTC", "RemoteUrl": "https://github.com/ropensci/babette", "RemoteRef": "main", "RemoteSha": "ea644a8a68c7e314130537caa2603e0acbe37207", "NeedsCompilation": "no", "Packaged": { "Date": "2026-04-12 06:50:55 UTC", "User": "root" }, "Author": "Richèl J.C. Bilderbeek [aut, cre] (ORCID:\n),\nJoëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,\nsee https://github.com/richelbilderbeek/onboarding/issues/209),\nDavid Winter [rev] (David reviewed the package for rOpenSci, see\nhttps://github.com/richelbilderbeek/onboarding/issues/209),\nJason Griffiths [ctb] (ORCID: ),\nOlivier Roy [ctb],\nTanmay Dimri [ctb],\nGiovanni Laudanno [ctb]", "Maintainer": "Richèl J.C. Bilderbeek ", "MD5sum": "edbc0f9e9d8dae4bbc927b99cc420cbe", "_user": "ropensci", "_type": "src", "_file": "babette_2.3.5.tar.gz", "_fileid": "f2e60038ad245a6cf35dc6cfef88c73e2924aed0e271aadadd4e71eda34fe7a2", "_filesize": 2224992, "_sha256": "f2e60038ad245a6cf35dc6cfef88c73e2924aed0e271aadadd4e71eda34fe7a2", "_created": "2026-04-12T06:50:55.000Z", "_published": "2026-04-12T06:54:19.228Z", "_distro": "noble", "_jobs": [ { "job": 70953883224, "time": 160, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "6390923229" }, { "job": 70953883230, "time": 150, "config": "linux-release-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "6390922389" }, { "job": 70953883213, "time": 93, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6390917546" }, { "job": 70953883219, "time": 91, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6390917319" }, { "job": 70953716121, "time": 197, "config": "pkgdown", "r": "4.5.2", "check": "OK", "artifact": "6390905099" }, { "job": 70953716119, "time": 236, "config": "source", "r": "4.5.3", "check": "OK", "artifact": "6390908920" }, { "job": 70953883205, "time": 139, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "6390921440" }, { "job": 70953883233, "time": 132, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6390920995" }, { "job": 70953883228, "time": 82, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6390916503" }, { "job": 70953883216, "time": 81, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6390916477" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/babette", "_commit": { "id": "ea644a8a68c7e314130537caa2603e0acbe37207", "author": "richelbilderbeek ", "committer": "richelbilderbeek ", "message": "Fix links\n", "time": 1773382964 }, "_maintainer": { "name": "Richèl J.C. Bilderbeek", "email": "rjcbilderbeek@gmail.com", "login": "richelbilderbeek", "orcid": "0000-0003-1107-7049", "uuid": 2098230 }, "_registered": true, "_dependencies": [ { "package": "beautier", "version": ">= 2.6.13", "role": "Depends" }, { "package": "beastier", "version": ">= 2.5", "role": "Depends" }, { "package": "mauricer", "version": ">= 2.5.2", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "tracerer", "role": "Depends" }, { "package": "phangorn", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1.0", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.50", "role": "Suggests" }, { "package": "lintr", "role": "Suggests" }, { "package": "nLTT", "role": "Suggests" }, { "package": "rappdirs", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "readr", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-15", "n": 1 }, { "week": "2025-18", "n": 1 }, { "week": "2025-20", "n": 1 }, { "week": "2025-24", "n": 1 }, { "week": "2025-30", "n": 1 }, { "week": "2025-32", "n": 1 }, { "week": "2025-34", "n": 1 }, { "week": "2025-44", "n": 1 }, { "week": "2025-51", "n": 1 }, { "week": "2026-10", "n": 2 }, { "week": "2026-11", "n": 1 } ], "_tags": [], "_topics": [ "bayesian-inference", "beast2", "phylogenetics", "openjdk" ], "_stars": 46, "_contributors": [ { "user": "richelbilderbeek", "count": 34, "uuid": 2098230 }, { "user": "tanmaydimrigsoc", "count": 10, "uuid": 105608756 }, { "user": "olivroy", "count": 9, "uuid": 52606734 }, { "user": "giappo", "count": 3, "uuid": 14541948 }, { "user": "kant", "count": 1, "uuid": 32717 }, { "user": "jeroen", "count": 1, "uuid": 216319 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 444, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/babette" }, "_mentions": 1, "_devurl": "https://github.com/ropensci/babette", "_pkgdown": "https://docs.ropensci.org/babette/", "_searchresults": 64, "_metadata": { "review": { "id": 209, "status": "reviewed", "version": "1.2.2", "organization": "rOpenSci Software Review", "url": "https://github.com/ropensci/software-review/issues/209" }, "ropensci_category": "scalereprod" }, "_rbuild": "4.5.3", "_assets": [ "extra/babette.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/ropensci/babette", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "2.1.1", "date": "2020-01-11" }, { "version": "2.1.2", "date": "2020-02-01" }, { "version": "2.1.4", "date": "2020-08-11" }, { "version": "2.2", "date": "2020-11-06" }, { "version": "2.3", "date": "2021-09-27" }, { "version": "2.3.1", "date": "2022-06-21" }, { "version": "2.3.2", "date": "2022-08-12" }, { "version": "2.3.3", "date": "2023-09-27" }, { "version": "2.3.4", "date": "2024-06-25" } ], "_exports": [ "bbt_continue", "bbt_delete_temp_files", "bbt_run", "bbt_run_from_model", "bbt_self_test", "check_beast2_pkgs", "create_test_bbt_run_output", "create_test_ns_output", "get_alignment_ids_from_xml", "get_babette_path", "get_babette_paths", "is_dropbox_path", "parse_beast2_output", "parse_beast2_output_to_ns", "plot_densitree", "prepare_file_creation", "update_babette", "warn_if_dropbox" ], "_help": [ { "page": "bbt_continue", "title": "Continue a BEAST2 run", "topics": [ "bbt_continue" ] }, { "page": "bbt_delete_temp_files", "title": "Delete all the temporary files created by bbt_run_from_model", "topics": [ "bbt_delete_temp_files" ] }, { "page": "bbt_run", "title": "Run BEAST2", "topics": [ "bbt_run" ] }, { "page": "bbt_run_from_model", "title": "Run BEAST2", "topics": [ "bbt_run_from_model" ] }, { "page": "bbt_self_test", "title": "Do a self test to verify babette that works correctly.", "topics": [ "bbt_self_test" ] }, { "page": "check_beast2_pkgs", "title": "Checks if 'bbt_run' has the 'BEAST2' packages needed to process its arguments. Will stop if not.", "topics": [ "check_beast2_pkgs" ] }, { "page": "create_test_bbt_run_output", "title": "Get an example output of 'bbt_run' or 'bbt_run_from_model'.", "topics": [ "create_test_bbt_run_output" ] }, { "page": "create_test_ns_output", "title": "Create NS testing output", "topics": [ "create_test_ns_output" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "get_alignment_ids_from_xml", "title": "Get the alignment IDs from one or more 'BEAST2' XML input files.", "topics": [ "get_alignment_ids_from_xml" ] }, { "page": "get_babette_path", "title": "Get the full path of a file in the 'inst/extdata' folder", "topics": [ "get_babette_path" ] }, { "page": "get_babette_paths", "title": "Get the full paths of files in the 'inst/extdata' folder", "topics": [ "get_babette_paths" ] }, { "page": "is_dropbox_path", "title": "Detect if a path is inside a Dropbox-backed folder", "topics": [ "is_dropbox_path" ] }, { "page": "parse_beast2_output", "title": "Process the 'BEAST2' output dependent on 'BEAST2' package specifics", "topics": [ "parse_beast2_output" ] }, { "page": "parse_beast2_output_to_ns", "title": "Parse BEAST2 NS output", "topics": [ "parse_beast2_output_to_ns" ] }, { "page": "plot_densitree", "title": "Draw multiple trees on top of one another.", "topics": [ "plot_densitree" ] }, { "page": "prepare_file_creation", "title": "Internal function to prepare for 'BEAST2' creating files", "topics": [ "prepare_file_creation" ] }, { "page": "update_babette", "title": "Deprecated function.", "topics": [ "update_babette" ] }, { "page": "warn_if_dropbox", "title": "Warn when using files in a Dropbox-backed folder", "topics": [ "warn_if_dropbox" ] } ], "_readme": "https://github.com/ropensci/babette/raw/main/README.md", "_rundeps": [ "ade4", "ape", "beastier", "beautier", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "digest", "fastmatch", "generics", "glue", "hms", "igraph", "jsonlite", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "mauricer", "nlme", "phangorn", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "purrr", "quadprog", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "readr", "rJava", "rlang", "segmented", "seqinr", "sessioninfo", "sp", "stringi", "stringr", "tibble", "tidyselect", "tracerer", "tzdb", "utf8", "vctrs", "vroom", "withr", "xml2" ], "_sysdeps": [ { "shlib": "libjvm", "package": "openjdk-21-jre-headless", "headers": "openjdk-21-jre-headless", "source": "openjdk", "version": "21.0.10+7-1~24.04", "name": "openjdk", "homepage": "https://openjdk.java.net/", "description": "OpenJDK Java runtime, using Hotspot JIT (headless)" } ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "babette demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Let babette run 'BEAST2'", "Plot the posterior estimates", "Show the effective sample sizes (ESS)", "Show the summary statistics", "Plot the posterior phylogenies" ], "created": "2018-01-30 14:03:56", "modified": "2022-06-20 08:56:11", "commits": 43 }, { "source": "tutorial.Rmd", "filename": "tutorial.html", "title": "babette Tutorial", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "fasta_filename", "inference_model and mcmc", "site_model", "clock_model", "tree_prior", "mrca_prior" ], "created": "2018-07-07 17:38:24", "modified": "2023-12-27 11:17:19", "commits": 27 }, { "source": "step_by_step.Rmd", "filename": "step_by_step.html", "title": "babette: Step by Step", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Create a 'BEAST2' input file", "Display (part of) the 'BEAST2' input file", "Run MCMC", "Display (part of) the 'BEAST2' output files", "Parse output" ], "created": "2018-05-07 08:56:01", "modified": "2023-12-27 11:17:19", "commits": 28 }, { "source": "examples.Rmd", "filename": "examples.html", "title": "Examples", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example #1: all default", "Example #2: using an MRCA prior to specify a crown age", "Example #3: JC69 site model", "Example #4: Relaxed clock log normal", "Example #5: Birth-Death tree prior", "Example #6: Yule tree prior with a normally distributed birth rate", "Example #7: HKY site model with a non-zero proportion of invariants", "Example #8: Strict clock with a known clock rate" ], "created": "2018-02-07 06:34:02", "modified": "2022-06-20 08:56:11", "commits": 36 }, { "source": "nested_sampling.Rmd", "filename": "nested_sampling.html", "title": "Nested Sampling", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Experiment", "Do the run", "References" ], "created": "2018-09-12 07:18:04", "modified": "2023-12-27 11:17:19", "commits": 30 } ], "_score": 9.084361758551406, "_indexed": true, "_nocasepkg": "babette", "_universes": [ "ropensci", "richelbilderbeek" ], "_binaries": [ { "r": "4.6.0", "os": "linux", "version": "2.3.5", "date": "2026-04-12T06:53:32.000Z", "distro": "noble", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "071d27153c6f13275b71509349a2204db9fdfe5c3a47414df7eda77ce9d36c85", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.5.3", "os": "linux", "version": "2.3.5", "date": "2026-04-12T06:53:25.000Z", "distro": "noble", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "69f8a69667122203a50ffc0d47c1b6ff76947c7caad67b61cbdab17ccf6e1a79", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.5.3", "os": "mac", "version": "2.3.5", "date": "2026-04-12T06:52:36.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "3dcae6ae08c0fe61997be66cc96686cab850b15655ef11d0e5ca5ebe2d856ae4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.6.0", "os": "mac", "version": "2.3.5", "date": "2026-04-12T06:52:31.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "8445ffd64e1a4ee908b4083d184a979f3aed0fa6fe06acaf519dd7be621c1e5d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.5.1", "os": "wasm", "version": "2.3.5", "date": "2026-04-12T06:53:36.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "0cc6677d3cf69dcb350fea36a3268c0665bde5f1ff069fd22752e2c49c3c8306", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.7.0", "os": "win", "version": "2.3.5", "date": "2026-04-12T06:53:02.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "38ee4452a50f13c0425133de9f9c672892a6b6889918d94101173bdce913f626", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.5.3", "os": "win", "version": "2.3.5", "date": "2026-04-12T06:52:11.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "c2dae1e742a6b2eed51b268e38c643adfda49c4a5b9757e03890a71c2b4be73c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" }, { "r": "4.6.0", "os": "win", "version": "2.3.5", "date": "2026-04-12T06:52:11.000Z", "commit": "ea644a8a68c7e314130537caa2603e0acbe37207", "fileid": "1c655c84edb9086349190c9f72e4281180517d6a61103ff2f61a4fcc750b3a70", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/24300790999" } ] }