Changes in version 2.3.5                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - None

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.3.4 (2024-06-25)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Deprecate 'upgrade_babette', as this is against CRAN guidelines
      - All functions have their return value documented
      - Documentation links to other packages' documentation

BUG FIXES

  - Removed unused dependencies, and testthat dependency outside tests.
      - Import rlang for checking conditions.

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.3.3 (2023-09-27)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Use new CITATION style

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.3.2 (2022-08-12)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Did usethis::use_package_doc()

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.3.1 (2022-06-21)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Fix newer CRAN warnings

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                  Changes in version 2.3 (2021-09-27)                   

NEW FEATURES

  - Use GitHub Actions as a continuous integration service

MINOR IMPROVEMENTS

  - Add URL to DESCRIPTION

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                  Changes in version 2.2 (2020-11-06)                   

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Do not run example code of internal function 'prepare_file_creation'
    on CRAN flavor r-oldrel-macos-x86_64

BUG FIXES

  - Can run BEAST2 and BEAST2 packages when these are installed at a
    custom location

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.1.4 (2020-08-11)                  

NEW FEATURES

  - CRAN version

MINOR IMPROVEMENTS

  - None

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 2.1.3                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - No testthat usage in documentation examples

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.1.2 (2020-02-01)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Use https of BEAST2 website
      - Building the package does not create temporary files in
        ~/.cache, fix #85

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                 Changes in version 2.1.1 (2020-01-11)                  

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Process feedback CRAN (Issue 81)
      - Renamed internal function names to be more descriptive

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - Remove arguments that are deprecated, as there is no CRAN version
    yet

                         Changes in version 2.1                         

NEW FEATURES

  - Follow the beastier v2.3 new interface, in which the log filenames
    are part of the MCMC (as created by create_mcmc)

MINOR IMPROVEMENTS

  - None

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - In create_beast2_options, output_log_filename and
    output_trees_filenames are removed as arguments. These values are
    set by the BEAST2 XML

                        Changes in version 2.0.3                        

NEW FEATURES

  - babette can run when the BEAST2 options request temporary files in
    sub-sub-subfolders

MINOR IMPROVEMENTS

  - Builds on Travis CI's Bionic distribution

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 2.0.2                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Fix spelling error

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 2.0.1                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Travis CI uses phangorns binary R package

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                         Changes in version 2.0                         

NEW FEATURES

  - Transferred GitHub repository ownership to ropensci
      - CRAN and rOpenSci release candidate

MINOR IMPROVEMENTS

  - Tagged for the academic article about babette

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 1.2.5                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - BEAST2 package management using mauricer works under Windows as well
      - babette indicates that BEAST2.exe cannot be run under Windows
      - 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

  - None

DEPRECATED AND DEFUNCT

  - Cannot use hyper parameters

# Deprecated: create a hyper parameter
create_lambda_param(value = 1.2, estimate = TRUE)

                        Changes in version 1.2.4                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Tagged for the academic article about babette

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 1.2.3                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Renamed run to bbt_run to reduce conflicts with other packages

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None

                        Changes in version 1.2.2                        

NEW FEATURES

  - None

MINOR IMPROVEMENTS

  - Follow all rOpenSci packaging guidelines

BUG FIXES

  - None

DEPRECATED AND DEFUNCT

  - None