NEWS

---

beautier 2.6.16

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.15

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Code coverage is 100.00%

BUG FIXES

• s_parameter_to_xml can handle an upper value of infinity
• create_s_parameter has NA as the default value for upper, as was already implicitly assumed when generating the BEAST2 XML

DEPRECATED AND DEFUNCT

• None

beautier 2.6.14

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Clean lint

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.13

NEW FEATURES

• Add is_beast2_input_file_with_tipdates to detect if a BEAST2 XML input files indeed has tip dates stored
• Add check_tipdates_file to test a tip date file is valid
• Add read_tipdates_file to read a tip date file

MINOR IMPROVEMENTS

• Clearer error message when the tab-separated tip dates file does not use a tab as a separator. Empty lines are allowed.
• Clearer error message when the tip dates file has a header. A header is not allowed.
• Improved documentation in check_ functions

BUG FIXES

• A tipdates_filename must either be NA or be a path to an existing file, reported at #108
• Fix #109

DEPRECATED AND DEFUNCT

• None

beautier 2.6.12 (2024-04-01)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Remove dependency on 'spelling'

BUG FIXES

• Fixes https://github.com/ropensci/babette/issues/106

DEPRECATED AND DEFUNCT

• None

beautier 2.6.11 (2023-11-02)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• CRAN version
• Improved documentation

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.10

NEW FEATURES

• Remove dependency on 'assertive'

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.9 (2023-09-24)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use new CITATION style

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.8

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Did usethis::use_package_doc()

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

NEW FEATURES

• None

MINOR IMPROVEMENTS

• create_strict_clock_model can also create a strict model from only a string (conversion from a double was already supported)
• create_mean_param can also create a mean parameter from only a string (conversion from a double was already supported)
• Add get_default_beast_namespace_v2_4 and get_default_beast_namespace_v2_6, to work well with create_beauti_options_v2_4 and create_beauti_options_v2_6 respectively

BUG FIXES

• Strict clock model's clock rate can have a normal distribution, #138

DEPRECATED AND DEFUNCT

• None

beautier 2.6.7

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• The clock rate distribution of a strict clock model can be set

DEPRECATED AND DEFUNCT

• None

beautier 2.6.6

NEW FEATURES

• Add create_freq_param/create_param_freq for the GTR, HKY and TN93 site models
• Add create_kappa_param/create_param_kappa for the HKY site model
• Add is_freq_param for the GTR, HKY and TN93 site models
• Add is_kappa_param for the HKY site model
• The clock rate of a strict clock model can be estimated

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• create_hky_site_model does not have kappa as an argument anymore: use kappa_param instead. Using kappa gives a proper deprecation message

beautier 2.6.5 (2022-08-11)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Doc does not link to absent functions
• No tests take more than 5 seconds on CRAN infrastructure

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Removed functions that were deprecated in v2.6.4

beautier 2.6.4 (2022-06-05)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• There is no 'beautier' temporary folder created by the tests, not the examples, to comply with CRAN policy

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.3

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• At the end of the tests, delete the 'beautier' temporary folder, thanks Brian Ripley

DEPRECATED AND DEFUNCT

• Filenames cannot have spaces

beautier 2.6.2 (2021-07-25)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• check_empty_beautier_folder works correctly on Windows

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.6.1

NEW FEATURES

• Added check_empty_beautier_folder to make sure no temporary files are created

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Removed all deprecated functions and function arguments that warn the user in the current CRAN version (v2.6)
• Internal functions clock_model_to_xml_prior_distr, tipdate_taxa_to_xml_tree, tree_priors_to_xml_operators work with infererence_model, deprecated other arguments
• Deprecated internal function clock_models_to_xml_prior_distr, redirect user to clock_model_to_xml_prior_distr
• Deprecated internal function tree_priors_to_xml_operators, redirect user to tree_prior_to_xml_operators
• Deprecated clock_models_to_xml_state, redirect user to clock_model_to_xml_state
• Deprecated clock_models_to_xml_operators, redirect user to clock_model_to_xml_operators
• Deprecated clock_models_to_xml_tracelog, redirect user to clock_model_to_xml_tracelog
• Deprecated mrca_priors_to_xml_tracelog, redirect user to mrca_prior_to_xml_tracelog
• Deprecated tree_models_to_xml_tracelog, redirect user to tree_model_to_tracelog_xml

beautier 2.6 (2021-05-23)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Make sure that no files are created in ~/.cache, fix #129

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.5.2 (2021-05-22)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Removed LazyData: true from DESCRIPTION

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.5.1

NEW FEATURES

• None

MINOR IMPROVEMENTS

• GitHub Actions scheduler tests package once per week

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.5

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use GitHub Actions to check build
• Check more setups, thanks @GaryNapier
• Better synergy with system2

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• phylo_to_xml_state removed
• site_models_to_xml_state gives a deprecation message
• tree_priors_to_xml_state gives a deprecation message
• mrca_priors_to_xml_state has the arguments mrca_prior and has_non_strict_clock_model replaced by inference_model

beautier 2.4 (2020-10-16)

NEW FEATURES

• Add inference_models vignette

MINOR IMPROVEMENTS

• Added create_ns_inference_model
• No testthat tests in examples

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.3.7 (2020-08-05)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Internal functions have better names
• More internal functions use an inference_model (instead of multiple elements of it)

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.3.6 (2020-05-06)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• Fix bug when using tipdating, thanks Katherine S. Walter, @ksw9

DEPRECATED AND DEFUNCT

• None

beautier 2.3.5 (2020-02-25)

NEW FEATURES

• Add get_mcmc_filenames and get_inference_model_filenames
• Add rename_mcmc_filenames and rename_inference_model_filenames
• Add rename functions get_remove_dir_fun, get_remove_hex_fun and get_replace_dir_fun

MINOR IMPROVEMENTS

• Link to https of BEAST2

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.3.4

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Lost dependency on orphaned geiger package

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Moved fasta_to_phylo and fastas_to_phylos to repository at https://github.com/richelbilderbeek/ribir to lose dependency on orphaned geiger package

beautier 2.3.3

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Implemented all @lintr-bot's suggestions

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.3.2 (2019-12-01)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• Remove files for CRAN submission

DEPRECATED AND DEFUNCT

• None

beautier 2.3.1

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use testthat in documentation, instead of the less known testit

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.3

NEW FEATURES

• Added create_tracelog, create_screenlog, create_treelog, that indicate where BEAST2 will store its output file
• create_mcmc has all elements that BEAUti has
• Added testing functions, that use a short MCMC chain length and/or a simple inference model: create_test_mcmc, create_test_tracelog, create_test_screenlog, create_test_treelog and create_test_inference_model

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.2.4

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Added create_beast2_input_from_model function

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.2.3

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Added check_mcmc_nested_sampling function

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.2.2

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Exported and documented more is_ functions
• Added check_file_exists function
• Added is_one_int and is_one_double functions

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 2.2.1 (2019-03-01)

NEW FEATURES

• beautier has passed rOpenSci peer review
• beautier is on CRAN

MINOR IMPROVEMENTS

• Exported multiple is_x and check_x functions

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 1.15

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• Correct BEAST2 files are created when using a RLN clock model, with an MRCA prior with a distribution, thanks @rscherrer and Jana Riederer

DEPRECATED AND DEFUNCT

• Support for multiple alignments, site models, clock models, tree models has decreased

beautier 1.14.2

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tested to build under macOS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 1.14.1

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Documented the simplified interface for parameters better
• Use the simplified interface for parameters as defaults more often

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 1.14.0

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Simplified interface for parameters:

# Old
distr <- create_distr_poisson(id = 1, lambda = create_lambda_param(value = 1.2))
# Added
distr <- create_distr_poisson(id = 1, lambda = 1.2)

BUG FIXES

• When using MRCA priors with/without monophyly with/without a distribution, resulted in incorrect BEAST2 .xml files

DEPRECATED AND DEFUNCT

• Cannot set parameters to be estimated, when the resulting BEAST2 .xml would be incomplete

beautier 1.13.4

NEW FEATURES

• Support for a Nested-Sampling MCMC run

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 1.13.3

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tagged for the academic article about babette

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

beautier 1.13.2

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Follow all rOpenSci packaging guidelines

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None