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beastier  

Call 'BEAST2'
View on CRAN: Click here


Download and install beastier package within the R console
Install from CRAN:
install.packages("beastier")

Install from Github:
library("remotes")
install_github("cran/beastier")

Install by package version:
library("remotes")
install_version("beastier", "2.5.2")



Attach the package and use:
library("beastier")
Maintained by
Richèl J.C. Bilderbeek
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-31
Latest Update: 2022-08-11
Description:
'BEAST2' () 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.
How to cite:
Richèl J.C. Bilderbeek (2019). beastier: Call 'BEAST2'. R package version 2.5.2, https://cran.r-project.org/web/packages/beastier. Accessed 22 Dec. 2024.
Previous versions and publish date:
2.0.14 (2019-05-31 12:00), 2.0.15 (2019-06-02 00:21), 2.1.1 (2019-12-02 13:50), 2.1.3 (2020-08-07 11:40), 2.2.1 (2020-10-30 15:50), 2.2 (2020-10-16 16:00), 2.4.2 (2021-06-05 18:40), 2.4.6 (2021-08-19 11:10), 2.4.7 (2021-09-07 16:00), 2.4.8 (2021-09-19 12:20), 2.4.9 (2022-06-03 10:50), 2.4.10 (2022-06-15 10:30), 2.4.11 (2022-08-11 16:40), 2.4.12 (2023-10-08 21:20), 2.4 (2021-05-23 11:50), 2.5.1 (2024-06-04 19:30), 2.5 (2023-11-07 13:50)
Other packages that cited beastier R package
View beastier citation profile
Other R packages that beastier depends, imports, suggests or enhances
Complete documentation for beastier
Functions, R codes and Examples using the beastier R package
Some associated functions: 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-package . beastier . 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 . default_params_doc . 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 . upgrade_beast2 . 
Some associated R codes: add_quotes_if_has_spaces.R . are_beast2_input_lines.R . are_identical_alignments.R . beast2_options_to_table.R . beastier-package.R . beastier.R . beastier_report.R . check_beast2.R . check_beast2_options.R . check_beast2_options_do_not_overwrite_existing_files.R . check_beast2_optionses.R . check_beast2_path.R . check_can_create_dir_for_state_output_file.R . check_can_create_file.R . check_can_create_screenlog_file.R . check_can_create_state_output_file.R . check_can_create_tracelog_file.R . check_can_create_treelog_file.R . check_empty_beastier_folder.R . check_empty_beaustier_folders.R . check_input_filename.R . check_n_threads.R . check_os.R . check_rng_seed.R . check_true_false.R . continue_beast2.R . create_beast2_continue_cmd_from_options.R . create_beast2_input_file_folder.R . create_beast2_options.R . create_beast2_run_cmd.R . create_beast2_run_cmd_from_options.R . create_beast2_screenlog_folder.R . create_beast2_state_output_file_folder.R . create_beast2_tracelog_folder.R . create_beast2_treelog_folder.R . create_beast2_validate_cmd.R . create_beast2_version_cmd.R . create_beastier_tempfolder.R . create_mcbette_beast2_options.R . create_random_alignment.R . create_random_fasta.R . create_random_phylogeny.R . create_temp_input_filename.R . create_temp_state_filename.R . default_params_doc.R . do_minimal_run.R . extract_screenlog_filename_from_beast2_input_file.R . extract_tracelog_filename_from_beast2_input_file.R . extract_treelog_filename_from_beast2_input_file.R . get_alignment_ids.R . get_beast2_example_filename.R . get_beast2_example_filenames.R . get_beast2_main_class_name.R . get_beast2_options_filenames.R . get_beast2_version.R . get_beastier_folder.R . get_beastier_tempfilename.R . get_default_beast2_bin_path.R . get_default_beast2_download_url.R . get_default_beast2_folder.R . get_default_beast2_jar_path.R . get_default_beast2_path.R . get_default_beast2_version.R . get_default_java_path.R . get_duplicate_param_ids.R . get_java_version.R . get_path.R . get_paths.R . get_trees_filenames.R . gives_beast2_warning.R . has_unique_ids.R . import-standalone-obj-type.R . import-standalone-types-check.R . install_beast2.R . is_alignment.R . is_beast2_input_file.R . is_beast2_installed.R . is_bin_path.R . is_jar_path.R . is_on_ci.R . print_beast2_options.R . remove_beastier_folder.R . remove_beaustier_folders.R . remove_file_if_present.R . rename_beast2_options_filenames.R . run_beast2.R . run_beast2_from_options.R . save_lines.R . save_nexus_as_fasta.R . uninstall_beast2.R . upgrade_beast2.R .  Full beastier package functions and examples
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