beautier v2.6.8 (2023-08-05)
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
andget_default_beast_namespace_v2_6
, to work well withcreate_beauti_options_v2_4
andcreate_beauti_options_v2_6
respectively
BUG FIXES
- Strict clock model’s clock rate can have a normal distribution, #138
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
beautier v2.6.5 (2022-08-11)
CRAN release: 2022-08-11
beautier v2.6.4 (2022-06-05)
CRAN release: 2022-06-05
beautier v2.6.1 (2021-07-23)
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 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
beautier v2.6 (2021-05-22)
CRAN release: 2021-05-23
MINOR IMPROVEMENTS
- Make sure that no files are created in
~/.cache
, fix #129
beautier v2.5 (2021-05-14)
MINOR IMPROVEMENTS
- Use GitHub Actions to check build
- Check more setups, thanks @GaryNapier
- Better synergy with
system2
beautier v2.3.7 (2020-08-05)
CRAN release: 2020-08-05
beautier v2.3.6 (2020-04-21)
CRAN release: 2020-05-06
BUG FIXES
- Fix bug when using tipdating, thanks Katherine S. Walter, @ksw9
beautier v2.3.5 (2020-02-25)
CRAN release: 2020-02-25
beautier v2.3.3 (2019-12-26)
MINOR IMPROVEMENTS
- Implemented all @lintr-bot’s suggestions
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
andcreate_test_inference_model
beautier v2.2.2 (2019-09-10)
beautier 1.15 (2018-11-10)
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
beautier 1.14.1 (2018-10-29)
beautier 1.14.0 (2018-10-26)
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)
beautier 1.13.4 (2018-09-11)
NEW FEATURES
- Support for a Nested-Sampling MCMC run
beautier 1.13.3 (2018-05-17)
MINOR IMPROVEMENTS
- Tagged for the academic article about
babette
beautier 1.13.2 (2018-04-05)
MINOR IMPROVEMENTS
- Follow all rOpenSci packaging guidelines