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Recent Releases of beastier

beastier - v2.5.2

beastier 2.5.2 (2025-08-10)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Corrected format in names in DESCRIPTION, thanks Kurt Hornik
  • Clean lint

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek 10 months ago

beastier - v2.5.1

  • Update email address of maintainer

- R
Published by richelbilderbeek almost 2 years ago

beastier - v2.5

  • Remove dependency on assertive
  • Follow newer CRAN guidelines

- R
Published by richelbilderbeek over 2 years ago

beastier - v2.4.12

New CRAN style

- R
Published by richelbilderbeek over 2 years ago

beastier - v2.4.11

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Add 'removebeaustierfolders' to delete both the 'beautier' and 'beastier' temporary folders
  • Add 'checkemptybeaustier_folders' to check that both the 'beautier' and 'beastier' temporary folders are empty

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • 'isonci' is now 'beautier::isonci'

- R
Published by richelbilderbeek almost 4 years ago

beastier - v2.4.9

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Also deletes the temporary 'beastier' folder

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 4 years ago

beastier - v2.4.8

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

- R
Published by richelbilderbeek over 4 years ago

beastier - v2.4.5

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Improved error handling
  • Less whitespace in beastier_report

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 5 years ago

beastier - v2.4.4

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Produces no undeleted temporary files

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 5 years ago

beastier - v2.4.3

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • check_can_create_file creates folder if needed

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 5 years ago

beastier - v2.4.2

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Cleans up all created temporary files
  • Tested to work on Windows

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 5 years ago

beastier - v2.4

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

- R
Published by richelbilderbeek about 5 years ago

beastier - v2.3.1

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

- R
Published by richelbilderbeek about 5 years ago

beastier - v2.3

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

- R
Published by richelbilderbeek about 5 years ago

beastier - v2.2.1

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

- R
Published by richelbilderbeek over 5 years ago

beastier - v2.2

### NEW FEATURES

  • Add 'createmcbettebeast2_options'

MINOR IMPROVEMENTS

  • No testthat tests in code examples

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek over 5 years ago

beastier - v2.1.3

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

- R
Published by richelbilderbeek almost 6 years ago

beastier - v2.1.2

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Documentation at rOpenSci to shows pictures

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.1.1

NEW FEATURES

  • Add vignettes

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.1

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

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.0.25

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

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.0.24

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

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.0.23

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

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.0.21

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

- R
Published by richelbilderbeek over 6 years ago

beastier - v2.0.20

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

- R
Published by richelbilderbeek almost 7 years ago

beastier - v2.0.19

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • check_beast2_options checks for duplicate filenames

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek almost 7 years ago

beastier - v2.0.18

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

- R
Published by richelbilderbeek almost 7 years ago

beastier - v2.0.15

  • 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

- R
Published by richelbilderbeek almost 7 years ago

beastier - v2.0.14

  • Add SystemRequirements field to DESCRIPTION

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.13

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

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.12

  • Package builds successfully without BEAST2 installed

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.11

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

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.10

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Passes tests without BEAST2 installed

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.9

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Pass local CRAN tests
  • Shortened examples' runtime

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.8

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Fix spelling error

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.7

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Documentation examples work on MacOS

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.6

  • Whitelist Schmirl

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.5

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

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.4

  • CRAN and rOpenSci candidate

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.3

  • CRAN and rOpenSci release candidate

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.2

  • CRAN and rOpenSci release candidate

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0.1

  • CRAN and rOpenSci candidate

- R
Published by richelbilderbeek about 7 years ago

beastier - v2.0

  • Moved to ropensci
  • CRAN and rOpenSci release candidate

- R
Published by richelbilderbeek over 7 years ago

beastier - v1.5.1.1

  • Passes CRAN checks that can be run on Travis

- R
Published by richelbilderbeek over 7 years ago

beastier - v1.5.1

- R
Published by richelbilderbeek over 7 years ago

beastier - v1.5

  • Works under Windows again, using beast.jar as the workhorse
  • Indicates that BEAST2.exe cannot be called under Windows

- R
Published by richelbilderbeek over 7 years ago

beastier - v1.4.4

  • Implemented rOpenSci feedback
  • 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.

- R
Published by richelbilderbeek almost 8 years ago

beastier - v1.4.3.1

Release to obtain Zenodo DOI.

- R
Published by richelbilderbeek about 8 years ago

beastier - v1.4.3

Tagged for the academic article about babette

- R
Published by richelbilderbeek about 8 years ago

beastier - v1.4

Fit for publication

- R
Published by richelbilderbeek about 8 years ago

beastier - v1.3

Fit for publication

- R
Published by richelbilderbeek about 8 years ago

beastier - v1.2

Fit for publication

- R
Published by richelbilderbeek about 8 years ago

beastier - v1.1

Works seamlessly as a sub-package of babette.

- R
Published by richelbilderbeek over 8 years ago

beastier - v1.0

- R
Published by richelbilderbeek over 8 years ago