{ "_id": "6990359c5fcc687c950d6e2b", "Package": "beastier", "Type": "Package", "Title": "Call 'BEAST2'", "Version": "2.5.3", "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/ropensci/onboarding/issues/209\"),\nperson(\"David\", \"Winter\", role = \"rev\", comment = \"David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209\"),\nperson(\"Jason\", \"Griffiths\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1667-8233\")),\nperson(\"Olivier\", \"Roy\", role = \"ctb\"),\nperson(\"Thijs\", \"Janzen\", role = \"ctb\"))", "Maintainer": "Richèl J.C. Bilderbeek ", "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 a command-line tool.\nThis package provides a way to call 'BEAST2' from an 'R'\nfunction call.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "URL": "https://docs.ropensci.org/beastier/ (website)\nhttps://github.com/ropensci/beastier/", "BugReports": "https://github.com/ropensci/beastier/issues", "Language": "en-US", "VignetteBuilder": "knitr", "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": "2025-12-08 18:23:47 UTC", "RemoteUrl": "https://github.com/ropensci/beastier", "RemoteRef": "main", "RemoteSha": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-02-14 08:39:43 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/ropensci/onboarding/issues/209),\nDavid Winter [rev] (David reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/onboarding/issues/209),\nJason Griffiths [ctb] (ORCID: ),\nOlivier Roy [ctb],\nThijs Janzen [ctb]", "MD5sum": "cfdf67f720874fbf46c8fec12c17f309", "_user": "ropensci", "_type": "src", "_file": "beastier_2.5.3.tar.gz", "_fileid": "2eb5cc2acfabe4f0ee2726c658bfc9a7b924720862791484abcfdb24fb402757", "_filesize": 700521, "_sha256": "2eb5cc2acfabe4f0ee2726c658bfc9a7b924720862791484abcfdb24fb402757", "_created": "2026-02-14T08:39:43.000Z", "_published": "2026-02-14T08:43:08.555Z", "_distro": "noble", "_jobs": [ { "job": 63613759986, "time": 148, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "5510068032" }, { "job": 63613760003, "time": 156, "config": "linux-release-x86_64", "r": "4.5.2", "check": "ERROR", "artifact": "5510068450" }, { "job": 63613759996, "time": 87, "config": "macos-devel-arm64", "r": "4.6.0", "check": "OK", "artifact": "5510064305" }, { "job": 63613760002, "time": 159, "config": "macos-release-arm64", "r": "4.5.2", "check": "OK", "artifact": "5510068673" }, { "job": 63613658814, "time": 150, "config": "pkgdown", "r": "4.5.2", "check": "OK", "artifact": "5510055810" }, { "job": 63613658815, "time": 204, "config": "source", "r": "4.5.2", "check": "OK", "artifact": "5510058938" }, { "job": 63613759992, "time": 129, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "5510066867" }, { "job": 63613760008, "time": 89, "config": "windows-devel", "r": "4.6.0", "check": "OK", "artifact": "5510064564" }, { "job": 63613760005, "time": 114, "config": "windows-oldrel", "r": "4.4.3", "check": "OK", "artifact": "5510066041" }, { "job": 63613760020, "time": 94, "config": "windows-release", "r": "4.5.2", "check": "OK", "artifact": "5510064752" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/beastier", "_commit": { "id": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "author": "richelbilderbeek ", "committer": "richelbilderbeek ", "message": "Fix Markdown\n", "time": 1765218227 }, "_maintainer": { "name": "Richèl J.C. Bilderbeek", "email": "rjcbilderbeek@gmail.com", "login": "richelbilderbeek", "orcid": "0000-0003-1107-7049", "uuid": 2098230 }, "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "beautier", "version": ">= 2.6.15", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "rappdirs", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rJava", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1.0", "role": "Imports" }, { "package": "sessioninfo", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "tracerer", "version": ">= 2.2.3", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-08", "n": 2 }, { "week": "2025-16", "n": 1 }, { "week": "2025-20", "n": 1 }, { "week": "2025-32", "n": 21 }, { "week": "2025-35", "n": 2 }, { "week": "2025-44", "n": 1 }, { "week": "2025-50", "n": 3 } ], "_tags": [ { "name": "v2.5.2", "date": "2025-08-10" } ], "_topics": [ "bayesian", "beast", "beast2", "phylogenetic-inference", "phylogenetics", "openjdk" ], "_stars": 11, "_contributors": [ { "user": "richelbilderbeek", "count": 71, "uuid": 2098230 }, { "user": "olivroy", "count": 8, "uuid": 52606734 }, { "user": "giappo", "count": 1, "uuid": 14541948 }, { "user": "jeroen", "count": 1, "uuid": 216319 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 428, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/beastier" }, "_devurl": "https://github.com/ropensci/beastier", "_pkgdown": "https://docs.ropensci.org/beastier/", "_searchresults": 51, "_metadata": { "ropensci_category": "scalereprod" }, "_rbuild": "4.5.2", "_assets": [ "extra/beastier.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/beastier", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "2.0.14", "date": "2019-05-31" }, { "version": "2.0.15", "date": "2019-06-01" }, { "version": "2.1.1", "date": "2019-12-02" }, { "version": "2.1.3", "date": "2020-08-07" }, { "version": "2.2", "date": "2020-10-16" }, { "version": "2.2.1", "date": "2020-10-30" }, { "version": "2.4", "date": "2021-05-23" }, { "version": "2.4.2", "date": "2021-06-05" }, { "version": "2.4.6", "date": "2021-08-19" }, { "version": "2.4.7", "date": "2021-09-07" }, { "version": "2.4.8", "date": "2021-09-19" }, { "version": "2.4.9", "date": "2022-06-03" }, { "version": "2.4.10", "date": "2022-06-15" }, { "version": "2.4.11", "date": "2022-08-11" }, { "version": "2.4.12", "date": "2023-10-08" }, { "version": "2.5", "date": "2023-11-07" }, { "version": "2.5.1", "date": "2024-06-04" }, { "version": "2.5.2", "date": "2024-10-06" } ], "_exports": [ "add_quotes_if_has_spaces", "are_beast2_input_lines", "are_beast2_input_lines_deep", "are_beast2_input_lines_fast", "are_identical_alignments", "beast2_options_to_table", "beastier_report", "check_beast2", "check_beast2_options", "check_beast2_options_data_types", "check_beast2_options_do_not_overwrite_existing_files", "check_beast2_options_filenames_differ", "check_beast2_options_names", "check_beast2_optionses", "check_beast2_path", "check_can_create_dir_for_state_output_file", "check_can_create_file", "check_can_create_screenlog_file", "check_can_create_state_output_file", "check_can_create_tracelog_file", "check_can_create_treelog_file", "check_empty_beastier_folder", "check_empty_beaustier_folders", "check_input_filename", "check_input_filename_validity", "check_n_threads", "check_os", "check_rng_seed", "continue_beast2", "create_beast2_continue_cmd_from_options", "create_beast2_input_file_folder", "create_beast2_options", "create_beast2_run_cmd", "create_beast2_run_cmd_from_options", "create_beast2_screenlog_folder", "create_beast2_state_output_file_folder", "create_beast2_tracelog_folder", "create_beast2_treelog_folder", "create_beast2_validate_cmd", "create_beast2_validate_cmd_bin", "create_beast2_validate_cmd_jar", "create_beast2_version_cmd", "create_beast2_version_cmd_bin", "create_beast2_version_cmd_jar", "create_beastier_tempfolder", "create_mcbette_beast2_options", "create_random_alignment", "create_random_fasta", "create_random_phylogeny", "create_temp_input_filename", "create_temp_state_filename", "do_minimal_run", "extract_screenlog_filename_from_beast2_input_file", "extract_tracelog_filename_from_beast2_input_file", "extract_treelog_filename_from_beast2_input_file", "get_alignment_ids_from_xml_filename", "get_beast2_example_filename", "get_beast2_example_filenames", "get_beast2_main_class_name", "get_beast2_options_filenames", "get_beast2_version", "get_beastier_folder", "get_beastier_path", "get_beastier_paths", "get_beastier_tempfilename", "get_default_beast2_bin_path", "get_default_beast2_download_url", "get_default_beast2_download_url_linux", "get_default_beast2_download_url_win", "get_default_beast2_folder", "get_default_beast2_jar_path", "get_default_beast2_path", "get_default_beast2_version", "get_default_java_path", "get_duplicate_param_ids", "get_java_version", "get_trees_filenames", "gives_beast2_warning", "has_unique_ids", "install_beast2", "is_alignment", "is_beast2_input_file", "is_beast2_installed", "is_bin_path", "is_jar_path", "is_on_appveyor", "is_on_ci", "is_on_travis", "is_win_bin_path", "print_beast2_options", "remove_beastier_folder", "remove_beaustier_folders", "remove_file_if_present", "rename_beast2_options_filenames", "run_beast2", "run_beast2_from_options", "save_lines", "save_nexus_as_fasta", "uninstall_beast2" ], "_help": [ { "page": "add_quotes_if_has_spaces", "title": "Add quotes around the string if it contains spaces.", "topics": [ "add_quotes_if_has_spaces" ] }, { "page": "are_beast2_input_lines", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines" ] }, { "page": "are_beast2_input_lines_deep", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines_deep" ] }, { "page": "are_beast2_input_lines_fast", "title": "Would these lines of text, when written to a file, result in a valid BEAST2 input file?", "topics": [ "are_beast2_input_lines_fast" ] }, { "page": "are_identical_alignments", "title": "Determines if the two alignments are equal", "topics": [ "are_identical_alignments" ] }, { "page": "beast2_options_to_table", "title": "Convert a 'beast2_options' to a table", "topics": [ "beast2_options_to_table" ] }, { "page": "beastier_report", "title": "Creates a beastier report", "topics": [ "beastier_report" ] }, { "page": "check_beast2", "title": "Check if 'BEAST2' is installed properly.", "topics": [ "check_beast2" ] }, { "page": "check_beast2_options", "title": "Check if the 'beast2_options' is a valid BEAST2 options object.", "topics": [ "check_beast2_options" ] }, { "page": "check_beast2_options_data_types", "title": "Check if the 'beast2_options', which is a list, has all elements of the right data types", "topics": [ "check_beast2_options_data_types" ] }, { "page": "check_beast2_options_do_not_overwrite_existing_files", "title": "Internal function", "topics": [ "check_beast2_options_do_not_overwrite_existing_files" ] }, { "page": "check_beast2_options_filenames_differ", "title": "Check if the filenames in 'beast2_options' differ", "topics": [ "check_beast2_options_filenames_differ" ] }, { "page": "check_beast2_options_names", "title": "Check if the 'beast2_options', which is a list, has all the elements needed.", "topics": [ "check_beast2_options_names" ] }, { "page": "check_beast2_optionses", "title": "Check if the 'beast2_options' is a valid BEAST2 options object.", "topics": [ "check_beast2_optionses" ] }, { "page": "check_beast2_path", "title": "Checks the BEAST2 '.jar' path. Will stop if there is a problem with the BEAST2 '.jar' path.", "topics": [ "check_beast2_path" ] }, { "page": "check_can_create_dir_for_state_output_file", "title": "Internal function", "topics": [ "check_can_create_dir_for_state_output_file" ] }, { "page": "check_can_create_file", "title": "Internal function", "topics": [ "check_can_create_file" ] }, { "page": "check_can_create_screenlog_file", "title": "Internal function", "topics": [ "check_can_create_screenlog_file" ] }, { "page": "check_can_create_state_output_file", "title": "Internal function", "topics": [ "check_can_create_state_output_file" ] }, { "page": "check_can_create_tracelog_file", "title": "Internal function to check if the MCMC's tracelog file can be created.", "topics": [ "check_can_create_tracelog_file" ] }, { "page": "check_can_create_treelog_file", "title": "Internal function", "topics": [ "check_can_create_treelog_file" ] }, { "page": "check_empty_beastier_folder", "title": "Check there are no files in the default beastier folder", "topics": [ "check_empty_beastier_folder" ] }, { "page": "check_empty_beaustier_folders", "title": "Check there are no files in the default `beautier` and `beastier` folders", "topics": [ "check_empty_beaustier_folders" ] }, { "page": "check_input_filename", "title": "Checks the input filename. Will stop if there is a problem with the input filename.", "topics": [ "check_input_filename" ] }, { "page": "check_input_filename_validity", "title": "Checks the input filename. Will stop if there is a problem with the input filename.", "topics": [ "check_input_filename_validity" ] }, { "page": "check_n_threads", "title": "Check if the input is a valid number of threads.", "topics": [ "check_n_threads" ] }, { "page": "check_os", "title": "Checks if the operating system is supported", "topics": [ "check_os" ] }, { "page": "check_rng_seed", "title": "Check if the input is a valid RNG seed.", "topics": [ "check_rng_seed" ] }, { "page": "continue_beast2", "title": "Continue a BEAST2 run", "topics": [ "continue_beast2" ] }, { "page": "create_beast2_continue_cmd_from_options", "title": "Creates the terminal command to run BEAST2 from a 'beast2_options'", "topics": [ "create_beast2_continue_cmd_from_options" ] }, { "page": "create_beast2_input_file_folder", "title": "Create the folder where the BEAST2 input file will be created", "topics": [ "create_beast2_input_file_folder" ] }, { "page": "create_beast2_options", "title": "Function to create a set of BEAST2 options.", "topics": [ "create_beast2_options" ] }, { "page": "create_beast2_run_cmd", "title": "Creates the terminal command to run BEAST2", "topics": [ "create_beast2_run_cmd" ] }, { "page": "create_beast2_run_cmd_from_options", "title": "Creates the terminal command to run BEAST2 from a 'beast2_options'", "topics": [ "create_beast2_run_cmd_from_options" ] }, { "page": "create_beast2_screenlog_folder", "title": "Internal function", "topics": [ "create_beast2_screenlog_folder" ] }, { "page": "create_beast2_state_output_file_folder", "title": "Create the folder where the BEAST2 state output file will be created", "topics": [ "create_beast2_state_output_file_folder" ] }, { "page": "create_beast2_tracelog_folder", "title": "Internal function", "topics": [ "create_beast2_tracelog_folder" ] }, { "page": "create_beast2_treelog_folder", "title": "Internal function", "topics": [ "create_beast2_treelog_folder" ] }, { "page": "create_beast2_validate_cmd", "title": "Creates the terminal command to validate a BEAST2 input file", "topics": [ "create_beast2_validate_cmd" ] }, { "page": "create_beast2_validate_cmd_bin", "title": "Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_validate_cmd_bin" ] }, { "page": "create_beast2_validate_cmd_jar", "title": "Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_validate_cmd_jar" ] }, { "page": "create_beast2_version_cmd", "title": "Creates the terminal command to version a BEAST2 input file", "topics": [ "create_beast2_version_cmd" ] }, { "page": "create_beast2_version_cmd_bin", "title": "Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_version_cmd_bin" ] }, { "page": "create_beast2_version_cmd_jar", "title": "Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file", "topics": [ "create_beast2_version_cmd_jar" ] }, { "page": "create_beastier_tempfolder", "title": "Create the temporary folder as used by beastier", "topics": [ "create_beastier_tempfolder" ] }, { "page": "create_mcbette_beast2_options", "title": "Create a `beast2_options` structure for the `mcbette` R package", "topics": [ "create_mcbette_beast2_options" ] }, { "page": "create_random_alignment", "title": "Create a random alignment", "topics": [ "create_random_alignment" ] }, { "page": "create_random_fasta", "title": "Create a random FASTA file", "topics": [ "create_random_fasta" ] }, { "page": "create_random_phylogeny", "title": "Create a random phylogeny", "topics": [ "create_random_phylogeny" ] }, { "page": "create_temp_input_filename", "title": "Create a temporary filename for the BEAST2 XML filename", "topics": [ "create_temp_input_filename" ] }, { "page": "create_temp_state_filename", "title": "Create a temporary file for the BEAST2 XML output file that stores its state.", "topics": [ "create_temp_state_filename" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "do_minimal_run", "title": "Do a minimal BEAST2 run", "topics": [ "do_minimal_run" ] }, { "page": "extract_screenlog_filename_from_beast2_input_file", "title": "Internal function to extract the screenlog filename for a BEAST2 input file", "topics": [ "extract_screenlog_filename_from_beast2_input_file" ] }, { "page": "extract_tracelog_filename_from_beast2_input_file", "title": "Internal function to extract the tracelog filename for a BEAST2 input file", "topics": [ "extract_tracelog_filename_from_beast2_input_file" ] }, { "page": "extract_treelog_filename_from_beast2_input_file", "title": "Internal function to extract the treelog filename for a BEAST2 input file", "topics": [ "extract_treelog_filename_from_beast2_input_file" ] }, { "page": "get_alignment_ids_from_xml_filename", "title": "Get the alignment ID from a file with one alignment", "topics": [ "get_alignment_ids_from_xml_filename" ] }, { "page": "get_beast2_example_filename", "title": "Get the full path of a BEAST2 example file", "topics": [ "get_beast2_example_filename" ] }, { "page": "get_beast2_example_filenames", "title": "Get a list with the full paths of all BEAST2 example filenames", "topics": [ "get_beast2_example_filenames" ] }, { "page": "get_beast2_main_class_name", "title": "Get the BEAST2 main class name.", "topics": [ "get_beast2_main_class_name" ] }, { "page": "get_beast2_options_filenames", "title": "Extract the filenames from a `beast2_options`", "topics": [ "get_beast2_options_filenames" ] }, { "page": "get_beast2_version", "title": "Get the BEAST2 version", "topics": [ "get_beast2_version" ] }, { "page": "get_beastier_folder", "title": "Get the path to the beastier temporary files folder", "topics": [ "get_beastier_folder" ] }, { "page": "get_beastier_path", "title": "Get the full path of a file in the 'inst/extdata' folder", "topics": [ "get_beastier_path" ] }, { "page": "get_beastier_paths", "title": "Get the full paths of files in the 'inst/extdata' folder", "topics": [ "get_beastier_paths" ] }, { "page": "get_beastier_tempfilename", "title": "Get a temporary filename", "topics": [ "get_beastier_tempfilename" ] }, { "page": "get_default_beast2_bin_path", "title": "Get the default BEAST2 binary file ('beast', that is) path", "topics": [ "get_default_beast2_bin_path" ] }, { "page": "get_default_beast2_download_url", "title": "Get the default BEAST2 download URL, which depends on the operating system", "topics": [ "get_default_beast2_download_url" ] }, { "page": "get_default_beast2_download_url_linux", "title": "Get the BEAST2 download URL for Linux", "topics": [ "get_default_beast2_download_url_linux" ] }, { "page": "get_default_beast2_download_url_win", "title": "Get the BEAST2 download URL for Windows", "topics": [ "get_default_beast2_download_url_win" ] }, { "page": "get_default_beast2_folder", "title": "Get the path to the folder where this package installs BEAST2 by default", "topics": [ "get_default_beast2_folder" ] }, { "page": "get_default_beast2_jar_path", "title": "Get the default BEAST2 jar file's path", "topics": [ "get_default_beast2_jar_path" ] }, { "page": "get_default_beast2_path", "title": "Get the default BEAST2 path", "topics": [ "get_default_beast2_path" ] }, { "page": "get_default_beast2_version", "title": "Get the default BEAST2 version that is used by beastier", "topics": [ "get_default_beast2_version" ] }, { "page": "get_default_java_path", "title": "Obtains the default path to the Java executable", "topics": [ "get_default_java_path" ] }, { "page": "get_duplicate_param_ids", "title": "Find duplicate 'RealParameter' IDs", "topics": [ "get_duplicate_param_ids" ] }, { "page": "get_java_version", "title": "Get the Java version", "topics": [ "get_java_version" ] }, { "page": "get_trees_filenames", "title": "Get the .trees filenames that BEAST2 will produce", "topics": [ "get_trees_filenames" ] }, { "page": "gives_beast2_warning", "title": "Determines if BEAST2 issues a warning when using the BEAST2 XML input file", "topics": [ "gives_beast2_warning" ] }, { "page": "has_unique_ids", "title": "Determine if the XML text has unique parameter IDs", "topics": [ "has_unique_ids" ] }, { "page": "install_beast2", "title": "Deprecated function to install BEAST2", "topics": [ "install_beast2" ] }, { "page": "is_alignment", "title": "Determines if the input is an alignment of type DNAbin", "topics": [ "is_alignment" ] }, { "page": "is_beast2_input_file", "title": "Is a file a valid BEAST2 input file?", "topics": [ "is_beast2_input_file" ] }, { "page": "is_beast2_installed", "title": "Checks if BEAST2 is installed", "topics": [ "is_beast2_installed" ] }, { "page": "is_bin_path", "title": "Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present", "topics": [ "is_bin_path" ] }, { "page": "is_jar_path", "title": "Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present", "topics": [ "is_jar_path" ] }, { "page": "is_on_appveyor", "title": "Deprecated function, use is_on_appveyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Deprecated function, use is_on_ci", "topics": [ "is_on_ci" ] }, { "page": "is_on_travis", "title": "Deprecated function, use is_on_travis", "topics": [ "is_on_travis" ] }, { "page": "is_win_bin_path", "title": "Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present", "topics": [ "is_win_bin_path" ] }, { "page": "print_beast2_options", "title": "Pretty-print a `beast2_options`", "topics": [ "print_beast2_options" ] }, { "page": "remove_beastier_folder", "title": "Check there are no files in the default beautier folder", "topics": [ "remove_beastier_folder" ] }, { "page": "remove_beaustier_folders", "title": "Remove the `beautier` and `beastier` temporary folders", "topics": [ "remove_beaustier_folders" ] }, { "page": "remove_file_if_present", "title": "Remove a file if it is present, will do nothing if it is not.", "topics": [ "remove_file_if_present" ] }, { "page": "rename_beast2_options_filenames", "title": "Rename the filenames in the BEAST2 options", "topics": [ "rename_beast2_options_filenames" ] }, { "page": "run_beast2", "title": "Run BEAST2", "topics": [ "run_beast2" ] }, { "page": "run_beast2_from_options", "title": "Run BEAST2", "topics": [ "run_beast2_from_options" ] }, { "page": "save_lines", "title": "Save text (a container of strings) to a file", "topics": [ "save_lines" ] }, { "page": "save_nexus_as_fasta", "title": "Save a NEXUS file as a FASTA file", "topics": [ "save_nexus_as_fasta" ] }, { "page": "uninstall_beast2", "title": "Deprecated function to uninstall BEAST2", "topics": [ "uninstall_beast2" ] }, { "page": "upgrade_beast2", "title": "Deprecated function to upgrade BEAST2.", "topics": [ "upgrade_beast2" ] } ], "_readme": "https://github.com/ropensci/beastier/raw/main/README.md", "_rundeps": [ "ade4", "ape", "beautier", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "digest", "fastmatch", "generics", "glue", "hms", "igraph", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "nlme", "phangorn", "pillar", "pixmap", "pkgconfig", "prettyunits", "progress", "purrr", "quadprog", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "readr", "rJava", "rlang", "segmented", "seqinr", "sessioninfo", "sp", "stringi", "stringr", "tibble", "tidyselect", "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": "beastier demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [ "Introduction" ], "created": "2019-04-25 12:10:51", "modified": "2022-06-01 19:17:20", "commits": 8 } ], "_score": 7.849333406373724, "_indexed": true, "_nocasepkg": "beastier", "_universes": [ "ropensci", "richelbilderbeek" ], "_binaries": [ { "r": "4.6.0", "os": "linux", "version": "2.5.3", "date": "2026-02-14T08:42:04.000Z", "distro": "noble", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "78e05360aed4ce6a5f601f1299b1f0a135e852772f833b7c186f8eb809f8b139", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.5.2", "os": "linux", "version": "2.5.3", "date": "2026-02-14T08:42:13.000Z", "distro": "noble", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "f3744664bb13a4f27d54d74dc388d29ede8260a671814aee36329d71e6c3ded6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.6.0", "os": "mac", "version": "2.5.3", "date": "2026-02-14T08:41:13.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "9665d9cb8c32b3fd6828c4697c4a6f773674cf1ae692db307ea013e456397942", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.5.2", "os": "mac", "version": "2.5.3", "date": "2026-02-14T08:42:13.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "1aeff0c288e703dcba3414d602eb88daad556bfd9a3a22e2c0548b244008c00b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.5.1", "os": "wasm", "version": "2.5.3", "date": "2026-02-14T08:42:11.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "77d960eb2d9cf81a8fec4e1d4df2b2eae32b92875f6bba3087eb04c07f2377bc", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.6.0", "os": "win", "version": "2.5.3", "date": "2026-02-14T08:41:00.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "2a954113923aa4a6bc7023100ab7d1049b7661ad4d125a3182bb025bc5216312", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.4.3", "os": "win", "version": "2.5.3", "date": "2026-02-14T08:41:13.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "5746bd3107c784e2604f44c46b70c5984d006ebafb70be798c66dfac3449b9c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" }, { "r": "4.5.2", "os": "win", "version": "2.5.3", "date": "2026-02-14T08:41:00.000Z", "commit": "fb20b891a5b85539ae1c6fc399c64cd381907fed", "fileid": "92f7c0137c5d954d1d84a2b3c2a8cce2c0c1f2180c8a947828d2a66888c3196a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/22014347104" } ] }