Changes in version 2.6.16 NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 2.6.14 NEW FEATURES - None MINOR IMPROVEMENTS - Clean lint BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 2.6.11 (2023-11-02) NEW FEATURES - None MINOR IMPROVEMENTS - CRAN version - Improved documentation BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.6.10 NEW FEATURES - Remove dependency on 'assertive' MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.6.9 (2023-09-24) NEW FEATURES - None MINOR IMPROVEMENTS - Use new CITATION style BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 2.5.2 (2021-05-22) NEW FEATURES - None MINOR IMPROVEMENTS - Removed LazyData: true from DESCRIPTION BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.5.1 NEW FEATURES - None MINOR IMPROVEMENTS - GitHub Actions scheduler tests package once per week BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 2.3.3 NEW FEATURES - None MINOR IMPROVEMENTS - Implemented all @lintr-bot's suggestions BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.3.2 (2019-12-01) NEW FEATURES - None MINOR IMPROVEMENTS - None BUG FIXES - Remove files for CRAN submission DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 2.2.4 NEW FEATURES - None MINOR IMPROVEMENTS - Added create_beast2_input_from_model function BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 2.2.3 NEW FEATURES - None MINOR IMPROVEMENTS - Added check_mcmc_nested_sampling function BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.14.2 NEW FEATURES - None MINOR IMPROVEMENTS - Tested to build under macOS BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 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 Changes in version 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 Changes in version 1.13.4 NEW FEATURES - Support for a Nested-Sampling MCMC run MINOR IMPROVEMENTS - None BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.13.3 NEW FEATURES - None MINOR IMPROVEMENTS - Tagged for the academic article about babette BUG FIXES - None DEPRECATED AND DEFUNCT - None Changes in version 1.13.2 NEW FEATURES - None MINOR IMPROVEMENTS - Follow all rOpenSci packaging guidelines BUG FIXES - None DEPRECATED AND DEFUNCT - None