NEWS.md

In dosreislab/bppr: An R package for BPP

News

Important changes to this project will be documented in this file.

[0.6.4] - 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

[0.6.3] - 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).

[0.6.2] - 2022-05-25

Added

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

[0.6.1] - 2020-11-29

Added

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

[0.6.0] - 2020-02-25

Changed

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

[0.5.3] - 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.

[0.5.2] - 2019-01-17

Changed

• Small changes to examples in msc2time and mcmc.summary

[0.5.1] - 2018-09-20

Added

• An additional example to the mcmc2densitree helpfile

[0.5.0] - 2018-09-20

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.

[0.4.0] - 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

dosreislab/bppr documentation built on April 13, 2025, 10:57 p.m.