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News

Newest versions at top.

pirouette 1.6.8 (2023-09-29)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • New CRAN submission

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.7 (2023-09-25)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Use new CITATION style

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.6 (submitted to CRAN)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.5 (unreleased)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Fix Imports #432
  • Fix sim_true_alignment example, that fails on Mac #432

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.4 (2020-11-24)

NEW FEATURES

  • Added check_pir_paramses to check a list of pir_params for validity
  • Add create_std_pir_paramses and create_std_pir_params to easily create one or more pir_params in a standard way
  • Add shorten_pir_params and shorten_pir_paramses to shorten run-time (for example, on Travis CI) easily
  • Add pir_save to save all pirouette output in a standarized way

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.3 (2020-02-26)

NEW FEATURES

  • Added pir_rename_to_std to conformize all files created by a pirouette run
  • Added 'pir_rename' to rename all files created by a pirouette run
  • Depend on beautier v2.3.5 (for rename_mcmc_filenames)

MINOR IMPROVEMENTS

  • Use at-least versions of packages, instead of exact versions
  • Check if there is need for an evidence file. Will stop if there is an evidence filename specified without needing one and vice versa

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • Use new nodeSube v0.5 (2020-01-13) default arguments

pirouette 1.6.2 (2020-01-06)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Process goodpractice feedback

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6.1 (2020-01-01)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Improved documentation
  • Increased code coverage
  • Removed dead code

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.6 (2019-10-13)

NEW FEATURES

  • Can create a twin tree that is a copy, by using copy_tree as the method used in create_twin_tree
  • Can use node substitution model, by using linked_node_sub (lns) or unlinked_node_sub (uns) as the site_model used in create_alignment

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.5.1 (2019-09-10)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Use mcbette version in which a higher number of particles in Nested Sampling does result in a better marginal likelihood estimation

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.5 (2019-08-19)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • Checks that all experiments have a unique inference model

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.4.1 (2019-08-19)

NEW FEATURES

  • None

MINOR IMPROVEMENTS

  • None

BUG FIXES

  • Table with evidences for twin models works

DEPRECATED AND DEFUNCT

  • None

pirouette 1.4 (2019-08-18)

NEW FEATURES

  • Evidence estimations shows estimated error of evidence
  • Evidence estimations shows effective sample size in estimating the evidence

MINOR IMPROVEMENTS

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

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None

pirouette 1.3 (2019-08-15)

NEW FEATURES

  • Removed duplicate evidence_epsilon argument from est_evidences: use the epsilon supplied in the experiments' est_evidence_mcmc$epsilon

MINOR IMPROVEMENTS

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

BUG FIXES

  • None

DEPRECATED AND DEFUNCT

  • None