Newest versions at top.
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- Corrected format in names in
DESCRIPTION, thanks Kurt Hornik
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- Update email address of maintainer
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- Remove dependency on 'assertive'
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- Use new CITATION style
- Did
usethis::use_package_doc()
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- 'is_on_ci' is now 'beautier::is_on_ci'
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- 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
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- Also deletes the temporary 'beastier' folder
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check_empty_beastier_folderworks under Windows
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- Allow to use treelog, screenlog and tracelog filenames in absent sub-sub-subfolders, fixes babette bug
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- Improved documentation, thanks Julia Haider
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- Improved error handling
- Less whitespace in
beastier_report
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- Produces no undeleted temporary files
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check_can_create_filecreates folder if needed
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- Tested to work on Windows
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- Cleans up all created temporary files
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install_beast2,upgrade_beast2,uninstall_beast2are deprecated, as these violated CRAN policy. Thanks to Brian Ripley for sharing! The deprecation message will point users to the non-officialbeastierinstallpackage athttps://github.com/richelbilderbeek/beastierinstall- Removed deprecated function
update_beastier
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- 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
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- Add
continue_beast2to continue a BEAST2 run
- Builds on GitHub Actions
- Added
is_on_github_actionsto detect the GitHub Actions environment is_on_cidetects the GitHub Actions environment
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update_beastier: gives deprecation message
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get_default_beast2_jar_pathallows for a custom folder nameinstall_beast2is silent by defaultinstall_beast2anduninstall_beast2give more information when verbose
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- Add 'create_mcbette_beast2_options'
- No
testthattests in code examples
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- Add
rename_beast2_options_filenames - Add
get_beast2_options_filenames - Allow tildes in file paths, for example
~/beast2.xml - Add
beastier_reportto help create a bug report - Can
install_beast2for a specific version
- Enable MacOS build again
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- Documentation at rOpenSci to shows pictures
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- Add vignettes
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- Follows
beautierv2.3 interface
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- The function arguments
beast2_output_log_filenameandbeast2_output_trees_filenamehave become obsolete. Usecreate_tracelog()$filenameandcreate_treelog()$filenameas part of an MCMC instead - The function argument
beast2_working_diris obsoleted, because it no longer served a purpose. Usesetwdto set the working directory
- Add
get_beast2_example_filenamesto get the full paths of all the BEAST2 example files - Add
get_beast2_example_filenameto get the full path of a BEAST2 example file - Add
get_default_beast2_working_dirto get the full path of the default BEAST2 working directory - Add
clear_beast2_working_dirto clear the BEAST2 working directory
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- Do not check if
beast2_pathstill/already exists incheck_beast2_options
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- Use BEAST2 main class name when calling the jar file, to fix the 'no main manifest attribute' error
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- Add
update_beastierto update thebeastierdependencies - Lowered cyclomatic complexity, thanks @lintr-bot
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create_beast2_optionschecks that the filenames are not in the same folder as the BEAST2 working directory
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- Added
get_beast2_options_filenamesto obtain the filenames in abeast2_options
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check_beast2_optionschecks for duplicate filenames
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- Install BEAST2
v2.6.0, instead ofv2.5.2
- Can create files in sub-sub-subfolders
- Builds on Travis CI distribution 'Bionic'
- Add
are_identical_alignments - Add
is_alignment
- RNG seed is checked to be a whole number (Issue #35, thanks @thijsjanzen)
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This version never had a formal release.
This version never had a formal release.
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- 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
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- Add
SystemRequirementsfield toDESCRIPTION
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- Install BEAST2
v2.5.2, instead ofv2.5.1 - Can call
run_beast2/run_beast2_from_optionsin parallel
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- Package builds successfully without BEAST2 installed
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get_default_beast2_bin_pathis silent if BEAST2 is absent- Package builds successfully without BEAST2 installed
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- Passes tests without BEAST2 installed
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- Pass local CRAN tests
- Shortened examples' runtime
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- Fix spelling error
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- Documentation examples work on macOS
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- Whitelist 'Schmirl'
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- CRAN and rOpenSci release candidate
- 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-3instead of also adding the fileLICENSE - Add examples to all functions
- In DESCRIPTION, use
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- CRAN and rOpenSci release candidate
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- GitHub repository is owned by
ropensci
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- Tested to work under macOS
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- Made up-to-date with newer version of
beautier
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- Instead of supplying a BEAST2
.jarpath (using the argumentbeast2_jar_path), one can now also supply the BEAST2 binary path.
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- All parameters named
beast2_jar_pathare now calledbeast2_path
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run_beast2had a parameter calledoverwrite_state_file, which is renamed tooverwriteand states if the.logfile and.treesfiles will be overwritten, like BEAST2 does. This is a bug fix, as the obsolete parameter name did not prevent the state file being overwritten.
- Calling
run_beast2with a parameter calledoverwrite_state_fileis obsolete. Use the parameteroverwriteinstead.
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- Tagged for the academic article about
babette
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- Follow all rOpenSci packaging guidelines
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