NEWS

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bppr 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

bppr 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).

bppr 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).

bppr 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.

bppr 2020-02-25 (2020-02-25)

Changed

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

bppr 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.

bppr 2019-01-17 (2019-01-17)

Changed

• Small changes to examples in msc2time and mcmc.summary

bppr 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.

bppr 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