beastier 2.5.2 (unreleased)
CRAN release: 2024-10-06
MINOR IMPROVEMENTS
- Corrected format in names in
DESCRIPTION, thanks Kurt Hornik
beastier 2.5.1 (2024-06-5)
CRAN release: 2024-06-04
MINOR IMPROVEMENTS
- Update email address of maintainer
beastier 2.5 (2023-11-07)
CRAN release: 2023-11-07
MINOR IMPROVEMENTS
- Remove dependency on ‘assertive’
beastier 2.4.12 (2023-09-25)
CRAN release: 2023-10-08
MINOR IMPROVEMENTS
- Use new CITATION style
- Did
usethis::use_package_doc()
beastier 2.4.11 (2022-08-11)
CRAN release: 2022-08-11
DEPRECATED AND DEFUNCT
- ‘is_on_ci’ is now ‘beautier::is_on_ci’
beastier 2.4.10 (2022-06-16)
CRAN release: 2022-06-15
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
beastier 2.4.9 (2022-06-03)
CRAN release: 2022-06-03
MINOR IMPROVEMENTS
- Also deletes the temporary ‘beastier’ folder
beastier 2.4.8 (2021-09-19)
CRAN release: 2021-09-19
MINOR IMPROVEMENTS
-
check_empty_beastier_folder works under Windows
beastier 2.4.7 (2021-09-06)
CRAN release: 2021-09-07
MINOR IMPROVEMENTS
- Allow to use treelog, screenlog and tracelog filenames in absent sub-sub-subfolders, fixes babette bug
beastier 2.4.6 (only released on CRAN)
CRAN release: 2021-08-19
MINOR IMPROVEMENTS
- Improved documentation, thanks Julia Haider
beastier 2.4.5 (2021-08-18)
MINOR IMPROVEMENTS
- Improved error handling
- Less whitespace in
beastier_report
beastier 2.4.4 (2021-08-17)
MINOR IMPROVEMENTS
- Produces no undeleted temporary files
beastier 2.4.3 (2021-07-09)
MINOR IMPROVEMENTS
-
check_can_create_file creates folder if needed
beastier 2.4.2 (2021-06-04)
CRAN release: 2021-06-05
MINOR IMPROVEMENTS
- Tested to work on Windows
beastier 2.4.1 (2021-05-30)
MINOR IMPROVEMENTS
- Cleans up all created temporary files
beastier 2.4 (2021-05-22)
CRAN release: 2021-05-23
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)
BUG FIXES
- Can correctly call BEAST2 when spaces in
- BEAST2 bin filename,
- BEAST2 jar filename,
- BEAST2 input filename
- BEAST2 state output filename. Thanks Jason Griffiths
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
DEPRECATED AND DEFUNCT
-
update_beastier: gives deprecation message
beastier 2.2.1 (2020-10-31)
CRAN release: 2020-10-30
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
beastier 2.2 (2020-10-16)
CRAN release: 2020-10-16
NEW FEATURES
- Add ‘create_mcbette_beast2_options’
MINOR IMPROVEMENTS
- No
testthat tests in code examples
beastier 2.1.3 (2020-08-05)
CRAN release: 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
beastier 2.1.2 (2020-01-06)
MINOR IMPROVEMENTS
- Documentation at rOpenSci to shows pictures
beastier 2.1.1 (2019-12-02)
CRAN release: 2019-12-02
beastier 2.1 (2019-10-27)
NEW FEATURES
- Follows
beautier v2.3 interface
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
beastier 2.0.24 (2019-09-30)
MINOR IMPROVEMENTS
- Do not check if
beast2_path still/already exists in check_beast2_options
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
beastier 2.0.22 (2019-09-16)
MINOR IMPROVEMENTS
- Add
update_beastier to update the beastier dependencies
- Lowered cyclomatic complexity, thanks @lintr-bot
beastier 2.0.21 (2019-09-10)
MINOR IMPROVEMENTS
-
create_beast2_options checks that the filenames are not in the same folder as the BEAST2 working directory
beastier 2.0.20 (2019-08-27)
MINOR IMPROVEMENTS
- Added
get_beast2_options_filenames to obtain the filenames in a beast2_options
beastier 2.0.19 (2019-08-23)
MINOR IMPROVEMENTS
-
check_beast2_options checks for duplicate filenames
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
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)
CRAN release: 2019-06-01
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
beastier 2.0.14 (2019-05-27)
CRAN release: 2019-05-31
MINOR IMPROVEMENTS
- Add
SystemRequirements field to DESCRIPTION
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
beastier 2.0.12 (2019-04-08)
MINOR IMPROVEMENTS
- Package builds successfully without BEAST2 installed
beastier 2.0.11 (2019-03-27)
MINOR IMPROVEMENTS
-
get_default_beast2_bin_path is silent if BEAST2 is absent
- Package builds successfully without BEAST2 installed
beastier 2.0.10 (2019-03-26)
MINOR IMPROVEMENTS
- Passes tests without BEAST2 installed
beastier 2.0.9 (2019-03-26)
MINOR IMPROVEMENTS
- Pass local CRAN tests
- Shortened examples’ runtime
beastier 2.0.8 (2019-03-26)
beastier 2.0.7 (2019-03-26)
MINOR IMPROVEMENTS
- Documentation examples work on macOS
beastier 2.0.6 (2019-03-25)
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
beastier 2.0.1 (2019-03-15)
NEW FEATURES
- CRAN and rOpenSci release candidate
beastier 2.0 (2019-01-04)
NEW FEATURES
- GitHub repository is owned by
ropensci
beastier 1.5.2 (2018-10-30)
MINOR IMPROVEMENTS
- Tested to work under macOS
beastier 1.5.1 (2018-10-26)
MINOR IMPROVEMENTS
- Made up-to-date with newer version of
beautier
beastier 1.5 (2018-09-12)
MINOR IMPROVEMENTS
- Instead of supplying a BEAST2
.jar path (using the argument beast2_jar_path), one can now also supply the BEAST2 binary path.
DEPRECATED AND DEFUNCT
- All parameters named
beast2_jar_path are now called beast2_path
beastier 1.4.4 (2018-08-05)
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)
beastier 1.4.2 (2018-04-05)
