Package: beastier 2.5.2
beastier: Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
Authors:
beastier_2.5.2.tar.gz
beastier_2.5.2.zip(r-4.5)beastier_2.5.2.zip(r-4.4)beastier_2.5.2.zip(r-4.3)
beastier_2.5.2.tgz(r-4.4-any)beastier_2.5.2.tgz(r-4.3-any)
beastier_2.5.2.tar.gz(r-4.5-noble)beastier_2.5.2.tar.gz(r-4.4-noble)
beastier_2.5.2.tgz(r-4.4-emscripten)beastier_2.5.2.tgz(r-4.3-emscripten)
beastier.pdf |beastier.html✨
beastier/json (API)
NEWS
# Install 'beastier' in R: |
install.packages('beastier', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/beastier/issues
bayesianbeastbeast2phylogenetic-inferencephylogenetics
Last updated 2 days agofrom:f9c5fa12e4. Checks:OK: 5 ERROR: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 06 2024 |
R-4.5-win | NOTE | Sep 06 2024 |
R-4.5-linux | ERROR | Sep 06 2024 |
R-4.4-win | OK | Sep 06 2024 |
R-4.4-mac | OK | Sep 06 2024 |
R-4.3-win | OK | Sep 06 2024 |
R-4.3-mac | OK | Sep 06 2024 |
Exports:add_quotes_if_has_spacesare_beast2_input_linesare_beast2_input_lines_deepare_beast2_input_lines_fastare_identical_alignmentsbeast2_options_to_tablebeastier_reportcheck_beast2check_beast2_optionscheck_beast2_options_data_typescheck_beast2_options_do_not_overwrite_existing_filescheck_beast2_options_filenames_differcheck_beast2_options_namescheck_beast2_optionsescheck_beast2_pathcheck_can_create_dir_for_state_output_filecheck_can_create_filecheck_can_create_screenlog_filecheck_can_create_state_output_filecheck_can_create_tracelog_filecheck_can_create_treelog_filecheck_empty_beastier_foldercheck_empty_beaustier_folderscheck_input_filenamecheck_input_filename_validitycheck_n_threadscheck_oscheck_rng_seedcontinue_beast2create_beast2_continue_cmd_from_optionscreate_beast2_input_file_foldercreate_beast2_optionscreate_beast2_run_cmdcreate_beast2_run_cmd_from_optionscreate_beast2_screenlog_foldercreate_beast2_state_output_file_foldercreate_beast2_tracelog_foldercreate_beast2_treelog_foldercreate_beast2_validate_cmdcreate_beast2_validate_cmd_bincreate_beast2_validate_cmd_jarcreate_beast2_version_cmdcreate_beast2_version_cmd_bincreate_beast2_version_cmd_jarcreate_beastier_tempfoldercreate_mcbette_beast2_optionscreate_random_alignmentcreate_random_fastacreate_random_phylogenycreate_temp_input_filenamecreate_temp_state_filenamedo_minimal_runextract_screenlog_filename_from_beast2_input_fileextract_tracelog_filename_from_beast2_input_fileextract_treelog_filename_from_beast2_input_fileget_alignment_ids_from_xml_filenameget_beast2_example_filenameget_beast2_example_filenamesget_beast2_main_class_nameget_beast2_options_filenamesget_beast2_versionget_beastier_folderget_beastier_pathget_beastier_pathsget_beastier_tempfilenameget_default_beast2_bin_pathget_default_beast2_download_urlget_default_beast2_download_url_linuxget_default_beast2_download_url_winget_default_beast2_folderget_default_beast2_jar_pathget_default_beast2_pathget_default_beast2_versionget_default_java_pathget_duplicate_param_idsget_java_versionget_trees_filenamesgives_beast2_warninghas_unique_idsinstall_beast2is_alignmentis_beast2_input_fileis_beast2_installedis_bin_pathis_jar_pathis_on_appveyoris_on_ciis_on_travisis_win_bin_pathprint_beast2_optionsremove_beastier_folderremove_beaustier_foldersremove_file_if_presentrename_beast2_options_filenamesrun_beast2run_beast2_from_optionssave_linessave_nexus_as_fastauninstall_beast2
Dependencies:ade4apebeautierbitbit64clicliprcolorspacecpp11crayondigestfansifarverfastmatchgenericsggplot2ggseqlogogluegtablehmsigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloreadrrJavarlangscalessegmentedseqinrsessioninfospstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithrxml2