Recent Releases of beautier
beautier - v2.6.15-pre-cran
beautier v2.6.15 (2025-08-08)
This is not a CRAN release, due to the CRAN team having holiday.
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Code coverage is 100.00%
BUG FIXES
s_parameter_to_xmlcan handle an upper value of infinitycreate_s_parameterhasNAas the default value forupper, as was already implicitly assumed when generating the BEAST2 XML
DEPRECATED AND DEFUNCT
- None
- R
Published by richelbilderbeek 5 months ago
beautier - v2.6.14-pre-cran
beautier v2.6.14 (2025-08-07)
This release will not end up on CRAN, as the CRAN team has holidays.
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Clean lint
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
- R
Published by richelbilderbeek 5 months ago
beautier - v2.6.13-pre-cran
beautier v2.6.13 (2025-08-05)
This release is not uploaded to CRAN yet, due to Summer holiday.
NEW FEATURES
- Add
is_beast2_input_file_with_tipdatesto detect if a BEAST2 XML input files indeed has tip dates stored - Add
check_tipdates_fileto test a tip date file is valid - Add
read_tipdates_fileto 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
DEPRECATED AND DEFUNCT
- None
- R
Published by richelbilderbeek 5 months ago
beautier - v2.6.1
NEW FEATURES
- Added
check_empty_beautier_folderto 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_operatorswork withinfererence_model, deprecated other arguments - Deprecated internal function
clock_models_to_xml_prior_distr, redirect user toclock_model_to_xml_prior_distr - Deprecated internal function
tree_priors_to_xml_operators, redirect user totree_prior_to_xml_operators - Deprecated
clock_models_to_xml_state, redirect user toclock_model_to_xml_state - Deprecated
clock_models_to_xml_operators, redirect user toclock_model_to_xml_operators - Deprecated
clock_models_to_xml_tracelog, redirect user toclock_model_to_xml_tracelog - Deprecated
mrca_priors_to_xml_tracelog, redirect user tomrca_prior_to_xml_tracelog - Deprecated
tree_models_to_xml_tracelog, redirect user totree_model_to_tracelog_xml
- R
Published by richelbilderbeek over 4 years ago
beautier - v2.5
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_stateremovedsite_models_to_xml_stategives a deprecation messagetree_priors_to_xml_stategives a deprecation messagemrca_priors_to_xml_statehas the argumentsmrca_priorandhas_non_strict_clock_modelreplaced byinference_model
- R
Published by richelbilderbeek over 4 years ago
beautier - v2.3.5
NEW FEATURES
- Add
get_mcmc_filenamesandget_inference_model_filenames - Add
rename_mcmc_filenamesandrename_inference_model_filenames - Add rename functions
get_remove_dir_fun,get_remove_hex_funandget_replace_dir_fun
MINOR IMPROVEMENTS
- Link to https of BEAST2
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
- R
Published by richelbilderbeek almost 6 years ago
beautier - v2.3.4
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Lost dependency on orphaned
geigerpackage
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Moved
fasta_to_phyloandfastas_to_phylosto repository athttps://github.com/richelbilderbeek/ribirto lose dependency on orphanedgeigerpackage
- R
Published by richelbilderbeek almost 6 years ago
beautier - v2.3
NEW FEATURES
- Added
create_tracelog,create_screenlog,create_treelog, that indicate where BEAST2 will store its output file create_mcmchas 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_treelogandcreate_test_inference_model
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
- R
Published by richelbilderbeek about 6 years ago
beautier - v1.14
- Implemented all feedback from rOpenSci
- Tested to build under Linux and Windows
- 100% code coverage
- R
Published by richelbilderbeek about 7 years ago
beautier - v1.13.3
Tagged for the academic article about babette
- R
Published by richelbilderbeek over 7 years ago
beautier - v1.11
- Minor bugfixes
- Improved function names, to better reflect their purpose
- Improved readability of functions, usually by shortening these
- Added more examples to documentation
- Check resulting XMLs for equivalence (instead of equality), to help improve readability and development speed
- Minor interface changes, mostly shortened argument names
- Functions that do not directly help using
create_beast2_inputare not exported anymore
- R
Published by richelbilderbeek about 8 years ago
beautier - v1.10
- Allows for a fixed crown age
- Supports all 4 site models: GTR, HKY, JC69, TN93
- Supports 2 clock models: relaxed log-normal and strict
- Supports 5 tree priors: Birth-Death, Coalescent Bayesian Skyline, Coalescent Constant Population, Coalescent Exponential Population, Yule
- Supports all 10 distributions: beta, exponential, gamma, inverse gamma, Laplace, log-normal, normal, 1/x, Poisson, uniform
- Supports all 10 different distributions's parameters (alpha, beta, clock rate, lambda, M, mean, mu, S, scale, sigma)
- Can use multiple alignments
- Can use different prior distribution for the 5 tree priors
- Thoroughly tested for single (possibly concatenated) alignment
- R
Published by richelbilderbeek about 8 years ago
beautier - v1.9
- Allows for a fixed crown age
- Supports all 4 site models: GTR, HKY, JC69, TN93
- Supports 2 clock models: relaxed log-normal and strict
- Supports 5 tree priors: Birth-Death, Coalescent Bayesian Skyline, Coalescent Constant Population, Coalescent Exponential Population, Yule
- Can use multiple alignments
- Can use different prior distribution for the 5 tree priors
- R
Published by richelbilderbeek about 8 years ago
beautier - v1.8
- Allows for a fixed crown age
- Supports all 4 site models: GTR, HKY, JC69, TN93
- Supports 2 clock models: relaxed log-normal and strict
- Supports 5 tree priors: Birth-Death, Coalescent Bayesian Skyline, Coalescent Constant Population, Coalescent Exponential Population, Yule
- Can use multiple alignments
- Can use different prior distribution for: Yule model's birth-rate
- R
Published by richelbilderbeek about 8 years ago