NEWS.md

In richelbilderbeek/beastier: Call 'BEAST2'

News

Newest versions at top.

beastier 2.5 (2023-11-07)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Remove dependency on 'assertive'

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.12 (2023-09-25)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use new CITATION style
• Did usethis::use_package_doc()

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 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'

beastier 2.4.10 (2022-06-16)

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

beastier 2.4.9 (2022-06-03)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Also deletes the temporary 'beastier' folder

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 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

beastier 2.4.7 (2021-09-06)

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

beastier 2.4.6 (only released on CRAN)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Improved documentation, thanks Julia Haider

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.5 (2021-08-18)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Improved error handling
• Less whitespace in beastier_report

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.4 (2021-08-17)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Produces no undeleted temporary files

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.3 (2021-07-09)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• check_can_create_file creates folder if needed

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.2 (2021-06-04)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tested to work on Windows

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4.1 (2021-05-30)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Cleans up all created temporary files

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.4 (2021-05-22)

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

beastier 2.3.1 (2021-05-15)

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

beastier 2.3 (2021-05-14)

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

beastier 2.2.1 (2020-10-31)

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

beastier 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

beastier 2.1.3 (2020-08-05)

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

beastier 2.1.2 (2020-01-06)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Documentation at rOpenSci to shows pictures

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.1.1 (2019-12-02)

NEW FEATURES

• Add vignettes

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.1 (2019-10-27)

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

beastier 2.0.25 (2019-10-10)

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

beastier 2.0.24 (2019-09-30)

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

beastier 2.0.23 (2019-09-29)

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

beastier 2.0.22 (2019-09-16)

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

beastier 2.0.21 (2019-09-10)

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

beastier 2.0.20 (2019-08-27)

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

beastier 2.0.19 (2019-08-23)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• check_beast2_options checks for duplicate filenames

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.18 (2019-08-14)

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

beastier 2.0.17

This version never had a formal release.

beastier 2.0.16

This version never had a formal release.

beastier 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

beastier 2.0.14 (2019-05-27)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Add SystemRequirements field to DESCRIPTION

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.13 (2019-05-14)

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

beastier 2.0.12 (2019-04-08)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Package builds successfully without BEAST2 installed

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.11 (2019-03-27)

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

beastier 2.0.10 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Passes tests without BEAST2 installed

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.9 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Pass local CRAN tests
• Shortened examples' runtime

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.8 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Fix spelling error

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.7 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Documentation examples work on macOS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.6 (2019-03-25)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Whitelist 'Schmirl'

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0.5 (2019-03-25)

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

beastier 2.0.1 (2019-03-15)

NEW FEATURES

• CRAN and rOpenSci release candidate

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 2.0 (2019-01-04)

NEW FEATURES

• GitHub repository is owned by ropensci

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 1.5.2 (2018-10-30)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tested to work under macOS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 1.5.1 (2018-10-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Made up-to-date with newer version of beautier

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 1.5 (2018-09-12)

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

beastier 1.4.4 (2018-08-05)

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.

beastier 1.4.3 (2018-05-17)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tagged for the academic article about babette

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beastier 1.4.2 (2018-04-05)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Follow all rOpenSci packaging guidelines

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

richelbilderbeek/beastier documentation built on Nov. 8, 2023, 9:29 p.m.