NEWS.md

In richelbilderbeek/mcbette: Model Comparison Using 'babette'

News

Newest versions at top.

mcbette 1.15.3 (2024-07-23)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Update email address

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.15.2 (2023-09-25)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use new CITATION style

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.15.1 (2022-10-28)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• Fix CRAN errors at https://github.com/ropensci/mcbette/issues/44

DEPRECATED AND DEFUNCT

• None

mcbette 1.15 (unreleased)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• Removed 'set_mcbette_state', as this violates CRAN policy

mcbette 1.14 (2021-05-14)

NEW FEATURES

• Use GitHub Actions as a continuous integration service

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.13 (2020-12-05)

NEW FEATURES

• Add plot_marg_liks

MINOR IMPROVEMENTS

• Add check_marg_liks

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.12 (2020-11-11)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Process CRAN feedback, thanks Gregor Seyer
• Use message instead of cat/print
• Fix URL in DESCRIPTION

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.11 (2020-10-16)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Depends on CRAN version of beautier (v2.4)

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.10 (2020-10-15)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Processed feedback rOpenSci
• Processed feedback JOSS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.9 (2020-10-10)

NEW FEATURES

• Transferred repository ownership to rOpenSci

MINOR IMPROVEMENTS

• Processed feedback rOpenSci
• Processed feedback JOSS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.8.4 (2020-05-21)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use CRAN versions of babette packages

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.8.3 (2020-02-24)

NEW FEATURES

• Add mcbette_self_test to self-test mcbette
• Add mcbette_report to print all information needed for a bug report
• Add get_mcbette_state and set_mcbette_state to store and restore the mcbette state. check_mcbette_state verifies if mcbette is in one of these three states: (1) both BEAST2 and the BEAST NS are installed, (2) only BEAST2 is installed (3) neither BEAST2 and the BEAST NS are installed

MINOR IMPROVEMENTS

• Separated the package mcbette from a script running it. The latter can be found at https://github.com/richelbilderbeek/mcbette_run
• Add README.Rmd, build README.md from it
• Add AppVeyor build, even though the core feature of mcbette requires Linux or MacOS

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.8.2 (2020-01-15)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Added can_run_mcbette as a shorthand for three if-statements
• Added create_ns_inference_model for convenience, as it is the same as create_inference_model(mcmc = create_ns_mcmc(...), ...). This function will be moved to beautier in a future version
• Vignette uses BEAST2 example alignment, instead of a simulated alignment
• Prepare for rOpenSci review
• Added more and better examples to the documentation

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.8.1 (2020-01-14)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Use CRAN version of babette

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.8 (2020-01-06)

NEW FEATURES

• Follow interface of beautier v2.3

MINOR IMPROVEMENTS

• Use CRAN versions of beautier, beastier, tracerer, mauricer
• Processed all @lintr-bot's comments

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.7 (2019-09-10)

NEW FEATURES

• Higher number of particles do result in a better estimation
• Renamed est_marg_liks_from_models to est_marg_liks, removed the old est_marg_liks

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.6 (2019-08-27)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Creates BEAST2 temporary files in same folder as the BEAST2 working folder. This allows mcbette to run on the Groninger Peregrine computer cluster

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.5 (2019-08-18)

NEW FEATURES

• Show effective sample size in marginal likelihood estimation

MINOR IMPROVEMENTS

• None

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.4 (2019-08-15)

NEW FEATURES

• Removed duplicate epsilon argument from est_marg_liks_from_model: use the epsilon supplied in the inference models' nested sampling MCMC

MINOR IMPROVEMENTS

• Better error message when using a CBS site model and too few taxa

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.3 (2019-08-14)

NEW FEATURES

• Added est_marg_lik to estimate a single marginal likelihood
• Disallow failed marginal likelihood estimations in est_marg_liks: the resulting table will never contain NAs

MINOR IMPROVEMENTS

• Better error message when using a CBS site model and too few taxa
• Builds on Bionic

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

mcbette 1.2

An untagged release

mcbette 1.1 (2019-05-29)

NEW FEATURES

• None

MINOR IMPROVEMENTS

• Travis builds on three operating systems

BUG FIXES

• None

DEPRECATED AND DEFUNCT

• None

richelbilderbeek/mcbette documentation built on Aug. 1, 2024, 11:09 p.m.