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Changelog

Source: NEWS.md

beautier v2.6.13 (unreleased)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • A tipdates_filename must either be NA or be a path to an existing file, reported here

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.12 (2024-04-01)

CRAN release: 2024-04-01

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Remove dependency on ‘spelling’

BUG FIXES

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.11 (2023-11-02)

CRAN release: 2023-11-02

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • CRAN version
  • Improved documentation

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.10 (2023-11-02)

NEW FEATURES

  • Remove dependency on ‘assertive’

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.9 (2023-09-25)

CRAN release: 2023-09-24

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Use new CITATION style

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.8 (2023-09-10)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Did usethis::use_package_doc()

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.8 (2023-08-05)

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 v2.6.7 (2023-04-05)

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 v2.6.6 (2023-03-14)

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 v2.6.5 (2022-08-11)

CRAN release: 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 v2.6.4 (2022-06-05)

CRAN release: 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 v2.6.3 (2022-05-18)

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 v2.6.2 (2021-07-24)

CRAN release: 2021-07-25

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • check_empty_beautier_folder works correctly on Windows

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.6.1 (2021-07-23)

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 v2.6 (2021-05-22)

CRAN release: 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 v2.5.2 (2021-05-22)

CRAN release: 2021-05-22

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Removed LazyData: true from DESCRIPTION

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.5.1 (2021-05-22)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • GitHub Actions scheduler tests package once per week

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.5 (2021-05-14)

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 v2.4 (2020-10-15)

CRAN release: 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 v2.3.7 (2020-08-05)

CRAN release: 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 v2.3.6 (2020-04-21)

CRAN release: 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 v2.3.5 (2020-02-25)

CRAN release: 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 v2.3.4 (2020-01-15)

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 v2.3.3 (2019-12-26)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.3.2 (2019-11-30)

CRAN release: 2019-12-01

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • Remove files for CRAN submission

DEPRECATED AND DEFUNCT

  • None

beautier v2.3.1 (2019-11-29)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

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

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.3 (2019-10-27)

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 v2.2.4 (2019-10-15)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Added create_beast2_input_from_model function

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.2.3 (2019-09-10)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Added check_mcmc_nested_sampling function

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier v2.2.2 (2019-09-10)

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 v2.2.1 (2019-03-08)

CRAN release: 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 (2018-11-10)

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 (2018-10-30)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Tested to build under macOS

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier 1.14.1 (2018-10-29)

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 (2018-10-26)

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 (2018-09-11)

NEW FEATURES

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier 1.13.3 (2018-05-17)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

beautier 1.13.2 (2018-04-05)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None