diff --git a/NEWS.md b/NEWS.md index 409185aa..1fb019e0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,123 +2,123 @@ Newest versions at top. -## beautier v2.6.13 (unreleased) +# beautier v2.6.13 (unreleased) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.12 (2024-04-01) +# beautier v2.6.12 (2024-04-01) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Remove dependency on 'spelling' -### BUG FIXES +## BUG FIXES * Fixes https://github.com/ropensci/babette/issues/106 -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.11 (2023-11-02) +# beautier v2.6.11 (2023-11-02) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * CRAN version * Improved documentation -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.10 (2023-11-02) +# beautier v2.6.10 (2023-11-02) -### NEW FEATURES +## NEW FEATURES * Remove dependency on 'assertive' -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.9 (2023-09-25) +# beautier v2.6.9 (2023-09-25) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Use new CITATION style -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.8 (2023-09-10) +# beautier v2.6.8 (2023-09-10) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Did `usethis::use_package_doc()` -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.8 (2023-08-05) +# beautier v2.6.8 (2023-08-05) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * `create_strict_clock_model` can also create a strict model from only a string (conversion from a double was already supported) @@ -128,36 +128,36 @@ Newest versions at top. to work well with `create_beauti_options_v2_4` and `create_beauti_options_v2_6` respectively -### BUG FIXES +## BUG FIXES * Strict clock model's clock rate can have a normal distribution, #138 -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.7 (2023-04-05) +# beautier v2.6.7 (2023-04-05) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * The clock rate distribution of a strict clock model can be set -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.6 (2023-03-14) +# beautier v2.6.6 (2023-03-14) -### NEW FEATURES +## 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 @@ -165,109 +165,109 @@ Newest versions at top. * Add `is_kappa_param` for the HKY site model * The clock rate of a strict clock model can be estimated -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## 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) +# beautier v2.6.5 (2022-08-11) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Doc does not link to absent functions * No tests take more than 5 seconds on CRAN infrastructure -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * Removed functions that were deprecated in v2.6.4 -## beautier v2.6.4 (2022-06-05) +# beautier v2.6.4 (2022-06-05) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * There is no 'beautier' temporary folder created by the tests, not the examples, to comply with CRAN policy -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.3 (2022-05-18) +# beautier v2.6.3 (2022-05-18) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * At the end of the tests, delete the 'beautier' temporary folder, thanks Brian Ripley -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * Filenames cannot have spaces -## beautier v2.6.2 (2021-07-24) +# beautier v2.6.2 (2021-07-24) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * `check_empty_beautier_folder` works correctly on Windows -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.6.1 (2021-07-23) +# beautier v2.6.1 (2021-07-23) -### NEW FEATURES +## NEW FEATURES * Added `check_empty_beautier_folder` to make sure no temporary files are created -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * Removed all deprecated functions and function arguments that warn the user in the current CRAN version (v2.6) @@ -290,77 +290,77 @@ Newest versions at top. * Deprecated `tree_models_to_xml_tracelog`, redirect user to `tree_model_to_tracelog_xml` -## beautier v2.6 (2021-05-22) +# beautier v2.6 (2021-05-22) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Make sure that no files are created in `~/.cache`, fix #129 -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.5.2 (2021-05-22) +# beautier v2.5.2 (2021-05-22) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Removed `LazyData: true` from DESCRIPTION -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.5.1 (2021-05-22) +# beautier v2.5.1 (2021-05-22) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * GitHub Actions scheduler tests package once per week -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.5 (2021-05-14) +# beautier v2.5 (2021-05-14) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Use GitHub Actions to check build * Check more setups, thanks @GaryNapier * Better synergy with `system2` -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * `phylo_to_xml_state` removed * `site_models_to_xml_state` gives a deprecation message @@ -368,160 +368,160 @@ Newest versions at top. * `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) +# beautier v2.4 (2020-10-15) -### NEW FEATURES +## NEW FEATURES * Add `inference_models` vignette -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Added `create_ns_inference_model` * No `testthat` tests in examples -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.7 (2020-08-05) +# beautier v2.3.7 (2020-08-05) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Internal functions have better names * More internal functions use an `inference_model` (instead of multiple elements of it) -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.6 (2020-04-21) +# beautier v2.3.6 (2020-04-21) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * Fix bug when using tipdating, thanks Katherine S. Walter, @ksw9 -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.5 (2020-02-25) +# beautier v2.3.5 (2020-02-25) -### NEW FEATURES +## 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 +## MINOR IMPROVEMENTS * Link to https of BEAST2 -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.4 (2020-01-15) +# beautier v2.3.4 (2020-01-15) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Lost dependency on orphaned `geiger` package -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## 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) +# beautier v2.3.3 (2019-12-26) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Implemented all @lintr-bot's suggestions -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.2 (2019-11-30) +# beautier v2.3.2 (2019-11-30) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * Remove files for CRAN submission -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3.1 (2019-11-29) +# beautier v2.3.1 (2019-11-29) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Use `testthat` in documentation, instead of the less known `testit` -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.3 (2019-10-27) +# beautier v2.3 (2019-10-27) -### NEW FEATURES +## NEW FEATURES * Added `create_tracelog`, `create_screenlog`, `create_treelog`, that indicate where BEAST2 will store its output file @@ -531,161 +531,161 @@ Newest versions at top. `create_test_screenlog`, `create_test_treelog` and `create_test_inference_model` -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.2.4 (2019-10-15) +# beautier v2.2.4 (2019-10-15) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Added `create_beast2_input_from_model` function -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.2.3 (2019-09-10) +# beautier v2.2.3 (2019-09-10) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Added `check_mcmc_nested_sampling` function -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.2.2 (2019-09-10) +# beautier v2.2.2 (2019-09-10) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Exported and documented more `is_` functions * Added `check_file_exists` function * Added `is_one_int` and `is_one_double` functions -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier v2.2.1 (2019-03-08) +# beautier v2.2.1 (2019-03-08) -### NEW FEATURES +## NEW FEATURES * `beautier` has passed rOpenSci peer review * `beautier` is on CRAN -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Exported multiple `is_x` and `check_x` functions -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier 1.15 (2018-11-10) +# beautier 1.15 (2018-11-10) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## 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 +## DEPRECATED AND DEFUNCT * Support for multiple alignments, site models, clock models, tree models has decreased -## beautier 1.14.2 (2018-10-30) +# beautier 1.14.2 (2018-10-30) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Tested to build under macOS -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier 1.14.1 (2018-10-29) +# beautier 1.14.1 (2018-10-29) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Documented the simplified interface for parameters better * Use the simplified interface for parameters as defaults more often -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier 1.14.0 (2018-10-26) +# beautier 1.14.0 (2018-10-26) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Simplified interface for parameters: @@ -696,66 +696,66 @@ distr <- create_distr_poisson(id = 1, lambda = create_lambda_param(value = 1.2)) distr <- create_distr_poisson(id = 1, lambda = 1.2) ``` -### BUG FIXES +## BUG FIXES * When using MRCA priors with/without monophyly with/without a distribution, resulted in incorrect BEAST2 `.xml` files -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * Cannot set parameters to be estimated, when the resulting BEAST2 `.xml` would be incomplete -## beautier 1.13.4 (2018-09-11) +# beautier 1.13.4 (2018-09-11) -### NEW FEATURES +## NEW FEATURES * Support for [a Nested-Sampling MCMC run](https://github.com/BEAST2-Dev/nested-sampling) -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * None -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier 1.13.3 (2018-05-17) +# beautier 1.13.3 (2018-05-17) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Tagged for [the academic article](https://github.com/richelbilderbeek/babette_article) about `babette` -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None -## beautier 1.13.2 (2018-04-05) +# beautier 1.13.2 (2018-04-05) -### NEW FEATURES +## NEW FEATURES * None -### MINOR IMPROVEMENTS +## MINOR IMPROVEMENTS * Follow all [rOpenSci packaging guidelines](https://github.com/ropensci/software-review/blob/master/packaging_guide.md) -### BUG FIXES +## BUG FIXES * None -### DEPRECATED AND DEFUNCT +## DEPRECATED AND DEFUNCT * None