Changes in version 2.5.3 NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.5.2 (2024-10-06) NEW FEATURES - None MINOR IMPROVEMENTS - Corrected format in names in DESCRIPTION, thanks Kurt Hornik - Clean lint BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.5.1 (2024-06-04) NEW FEATURES - None MINOR IMPROVEMENTS - Update email address of maintainer BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.5 (2023-11-07) NEW FEATURES - None MINOR IMPROVEMENTS - Remove dependency on 'assertive' BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.12 (2023-10-08) NEW FEATURES - None MINOR IMPROVEMENTS - Use new CITATION style - Did usethis::use_package_doc() BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.11 (2022-08-11) NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - 'is_on_ci' is now 'beautier::is_on_ci' Changes in version 2.4.10 (2022-06-15) NEW FEATURES - None MINOR IMPROVEMENTS - Add 'remove_beaustier_folders' to delete both the 'beautier' and 'beastier' temporary folders - Add 'check_empty_beaustier_folders' to check that both the 'beautier' and 'beastier' temporary folders are empty BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.9 (2022-06-03) NEW FEATURES - None MINOR IMPROVEMENTS - Also deletes the temporary 'beastier' folder BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.8 (2021-09-19) NEW FEATURES - None MINOR IMPROVEMENTS - check_empty_beastier_folder works under Windows BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.7 (2021-09-07) NEW FEATURES - None MINOR IMPROVEMENTS - Allow to use treelog, screenlog and tracelog filenames in absent sub-sub-subfolders, fixes babette bug BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.6 (2021-08-19) NEW FEATURES - None MINOR IMPROVEMENTS - Improved documentation, thanks Julia Haider BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.5 NEW FEATURES - None MINOR IMPROVEMENTS - Improved error handling - Less whitespace in beastier_report BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.4 NEW FEATURES - None MINOR IMPROVEMENTS - Produces no undeleted temporary files BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.3 NEW FEATURES - None MINOR IMPROVEMENTS - check_can_create_file creates folder if needed BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.2 (2021-06-05) NEW FEATURES - None MINOR IMPROVEMENTS - Tested to work on Windows BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4.1 NEW FEATURES - None MINOR IMPROVEMENTS - Cleans up all created temporary files BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.4 (2021-05-23) NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - install_beast2, upgrade_beast2, uninstall_beast2 are deprecated, as these violated CRAN policy. Thanks to Brian Ripley for sharing! The deprecation message will point users to the non-official beastierinstall package at https://github.com/richelbilderbeek/beastierinstall - Removed deprecated function update_beastier Changes in version 2.3.1 NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - Can correctly call BEAST2 when spaces in (1) BEAST2 bin filename, (2) BEAST2 jar filename, (3) BEAST2 input filename (4) BEAST2 state output filename. Thanks Jason Griffiths DEPRECATED AND DEFUNCT - None Changes in version 2.3 NEW FEATURES - Add continue_beast2 to continue a BEAST2 run MINOR IMPROVEMENTS - Builds on GitHub Actions - Added is_on_github_actions to detect the GitHub Actions environment - is_on_ci detects the GitHub Actions environment BUG FIXES - None DEPRECATED AND DEFUNCT - update_beastier: gives deprecation message Changes in version 2.2.1 (2020-10-30) NEW FEATURES - None MINOR IMPROVEMENTS - get_default_beast2_jar_path allows for a custom folder name - install_beast2 is silent by default - install_beast2 and uninstall_beast2 give more information when verbose BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.2 (2020-10-16) NEW FEATURES - Add 'create_mcbette_beast2_options' MINOR IMPROVEMENTS - No testthat tests in code examples BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.1.3 (2020-08-07) NEW FEATURES - Add rename_beast2_options_filenames - Add get_beast2_options_filenames - Allow tildes in file paths, for example ~/beast2.xml - Add beastier_report to help create a bug report - Can install_beast2 for a specific version MINOR IMPROVEMENTS - Enable MacOS build again BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.1.2 NEW FEATURES - None MINOR IMPROVEMENTS - Documentation at rOpenSci to shows pictures BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.1.1 (2019-12-02) NEW FEATURES - Add vignettes MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.1 NEW FEATURES - Follows beautier v2.3 interface MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - The function arguments beast2_output_log_filename and beast2_output_trees_filename have become obsolete. Use create_tracelog()$filename and create_treelog()$filename as part of an MCMC instead - The function argument beast2_working_dir is obsoleted, because it no longer served a purpose. Use setwd to set the working directory Changes in version 2.0.25 NEW FEATURES - Add get_beast2_example_filenames to get the full paths of all the BEAST2 example files - Add get_beast2_example_filename to get the full path of a BEAST2 example file - Add get_default_beast2_working_dir to get the full path of the default BEAST2 working directory - Add clear_beast2_working_dir to clear the BEAST2 working directory MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.24 NEW FEATURES - None MINOR IMPROVEMENTS - Do not check if beast2_path still/already exists in check_beast2_options BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.23 NEW FEATURES - Use BEAST2 main class name when calling the jar file, to fix the 'no main manifest attribute' error MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.22 NEW FEATURES - None MINOR IMPROVEMENTS - Add update_beastier to update the beastier dependencies - Lowered cyclomatic complexity, thanks @lintr-bot BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.21 NEW FEATURES - None MINOR IMPROVEMENTS - create_beast2_options checks that the filenames are not in the same folder as the BEAST2 working directory BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.20 NEW FEATURES - None MINOR IMPROVEMENTS - Added get_beast2_options_filenames to obtain the filenames in a beast2_options BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.19 NEW FEATURES - None MINOR IMPROVEMENTS - check_beast2_options checks for duplicate filenames BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.18 NEW FEATURES - Install BEAST2 v2.6.0, instead of v2.5.2 MINOR IMPROVEMENTS - Can create files in sub-sub-subfolders - Builds on Travis CI distribution 'Bionic' - Add are_identical_alignments - Add is_alignment BUG FIXES - RNG seed is checked to be a whole number (Issue #35, thanks @thijsjanzen) DEPRECATED AND DEFUNCT - None Changes in version 2.0.17 This version never had a formal release. Changes in version 2.0.16 This version never had a formal release. Changes in version 2.0.15 (2019-06-01) NEW FEATURES - None MINOR IMPROVEMENTS - Simplified run_beast2 - Improved error checking and logging in run_beast2 - Will overwrite files if requested (which is by default) - Removed example code that assumed all Linuxes have /home/username, thanks to Brian Ripley BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.14 (2019-05-31) NEW FEATURES - None MINOR IMPROVEMENTS - Add SystemRequirements field to DESCRIPTION BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.13 NEW FEATURES - Install BEAST2 v2.5.2, instead of v2.5.1 - Can call run_beast2/run_beast2_from_options in parallel MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.12 NEW FEATURES - None MINOR IMPROVEMENTS - Package builds successfully without BEAST2 installed BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.11 NEW FEATURES - None MINOR IMPROVEMENTS - get_default_beast2_bin_path is silent if BEAST2 is absent - Package builds successfully without BEAST2 installed BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.10 NEW FEATURES - None MINOR IMPROVEMENTS - Passes tests without BEAST2 installed BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.9 NEW FEATURES - None MINOR IMPROVEMENTS - Pass local CRAN tests - Shortened examples' runtime BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.8 NEW FEATURES - None MINOR IMPROVEMENTS - Fix spelling error BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.7 NEW FEATURES - None MINOR IMPROVEMENTS - Documentation examples work on macOS BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.6 NEW FEATURES - None MINOR IMPROVEMENTS - Whitelist 'Schmirl' BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.5 NEW FEATURES - CRAN and rOpenSci release candidate MINOR IMPROVEMENTS - Implemented feedback from CRAN, thanks Martina Schmirl: - In DESCRIPTION, use 'R' for programs - In DESCRIPTION, use four spaces - In DESCRIPTION, remove the redundant '... from R' in title - In DESCRIPTION, use only GPL-3 instead of also adding the file LICENSE - Add examples to all functions BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0.1 NEW FEATURES - CRAN and rOpenSci release candidate MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.0 NEW FEATURES - GitHub repository is owned by ropensci MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.5.2 NEW FEATURES - None MINOR IMPROVEMENTS - Tested to work under macOS BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.5.1 NEW FEATURES - None MINOR IMPROVEMENTS - Made up-to-date with newer version of beautier BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.5 NEW FEATURES - None MINOR IMPROVEMENTS - Instead of supplying a BEAST2 .jar path (using the argument beast2_jar_path), one can now also supply the BEAST2 binary path. BUG FIXES - None DEPRECATED AND DEFUNCT - All parameters named beast2_jar_path are now called beast2_path Changes in version 1.4.4 NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - run_beast2 had a parameter called overwrite_state_file, which is renamed to overwrite and states if the .log file and .trees files will be overwritten, like BEAST2 does. This is a bug fix, as the obsolete parameter name did not prevent the state file being overwritten. DEPRECATED AND DEFUNCT - Calling run_beast2 with a parameter called overwrite_state_file is obsolete. Use the parameter overwrite instead. Changes in version 1.4.3 NEW FEATURES - None MINOR IMPROVEMENTS - Tagged for the academic article about babette BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.4.2 NEW FEATURES - None MINOR IMPROVEMENTS - Follow all rOpenSci packaging guidelines BUG FIXES - None DEPRECATED AND DEFUNCT - None