NEWS.md

In richelbilderbeek/babette: Control 'BEAST2'

News

Newest versions at top.

babette v2.3.3 (2022-09-25)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use new CITATION style

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette v2.3.2 (2022-08-12)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Did usethis::use_package_doc()

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 2.3.1 (2022-06-21)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Fix newer CRAN warnings

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 2.3 (2021-05-14)

NEW FEATURES

• Use GitHub Actions as a continuous integration service

MINOR IMPROVEMENTS

• Add URL to DESCRIPTION

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 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

babette 2.1.4 (2020-08-11)

NEW FEATURES

• CRAN version

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 2.1.3 (2020-08-05)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• No testthat usage in documentation examples

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 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

babette 2.1.1 (2019-12-30)

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

babette 2.1 (2019-10-27)

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

babette 2.0.3 (2019-08-26)

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

babette 2.0.2 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Fix spelling error

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 2.0.1 (2019-03-26)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Travis CI uses phangorns binary R package

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 2.0 (2019-01-06)

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

babette 1.2.5 (2018-10-25)

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)

babette 1.2.4 (2018-05-17)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Tagged for the academic article about babette

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 1.2.3 (2018-05-04)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Renamed run to bbt_run to reduce conflicts with other packages

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

babette 1.2.2 (2018-04-05)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Follow all rOpenSci packaging guidelines

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

richelbilderbeek/babette documentation built on Oct. 10, 2023, 8:18 p.m.