mcmc2time.r so that a calendar time rate can be used to calibrate
the tree, by setting g.mean=1 and g.sd=0mcmc2densitree so that tip labels are correctly positioned in the
plot when extinct taxa are present (set using tip.ages).tip.ages to mcmc2densitree. This allows plotting trees with
sequences that have different sampling times (such as viruses).msc2time functions documentation using the
shifted log-normal distribution as a calibration density.bayes.factors so that it calculates parameteric bootstrap of
posterior probabilities. Updated documentation.glqrules) could not be found.
This meant method "gauss-quad" could not be used with the make.beta function.msc2time and mcmc.summarymcmc2densitree helpfilemcmc.summary to generate a summary (mean, CIs) from an MCMC sample
from BPP or MCMCTree.mcmc2densitree to plot a densi-tree using an MCMC sample from BPP
or MCMCTree.mcmc2multiphylo where the MCMC sample was not being thinned
correctly.mcmc2multiphylo to convert MCMC samples from BPP or MCMCTree to
lists of trees.Tags: Added, Changed, Deprecated, Removed, Fixed, Security