Changes in version 2025-04-11 (2025-04-11)               

Changed

  - Function mcmc2time.r so that a calendar time rate can be used to
    calibrate the tree, by setting g.mean=1 and g.sd=0

               Changes in version 2023-03-28 (2023-03-28)               

Fixed

  - Function mcmc2densitree so that tip labels are correctly positioned
    in the plot when extinct taxa are present (set using tip.ages).

               Changes in version 2022-05-25 (2022-05-25)               

Added

  - Argument tip.ages to mcmc2densitree. This allows plotting trees with
    sequences that have different sampling times (such as viruses).

               Changes in version 2020-11-29 (2020-11-29)               

Added

  - An additional example to the msc2time functions documentation using
    the shifted log-normal distribution as a calibration density.

               Changes in version 2020-02-25 (2020-02-25)               

Changed

  - Function bayes.factors so that it calculates parameteric bootstrap
    of posterior probabilities. Updated documentation.

               Changes in version 2019-11-12 (2019-11-12)               

Fixed

  - A bug where the Gaussian quadrature rules (glqrules) could not be
    found. This meant method "gauss-quad" could not be used with the
    make.beta function.

               Changes in version 2019-01-17 (2019-01-17)               

Changed

  - Small changes to examples in msc2time and mcmc.summary

               Changes in version 2018-09-20 (2018-09-20)               

Added

  - An additional example to the mcmc2densitree helpfile

Added

  - Function mcmc.summary to generate a summary (mean, CIs) from an MCMC
    sample from BPP or MCMCTree.
  - Function mcmc2densitree to plot a densi-tree using an MCMC sample
    from BPP or MCMCTree.

Fixed

  - A bug in mcmc2multiphylo where the MCMC sample was not being thinned
    correctly.

               Changes in version 2018-09-08 (2018-09-08)               

Added

  - Function mcmc2multiphylo to convert MCMC samples from BPP or
    MCMCTree to lists of trees.

Tags: Added, Changed, Deprecated, Removed, Fixed, Security