quantile.phybreak: Quantiles of sampled parameter values.

In donkeyshot/phybreak: Analysis of Outbreaks with Sequence Data

Description

Quantiles of sampled parameter values.

Usage

## S3 method for class 'phybreak'
quantile(x, whichpars = "posterior",
  probs = c(0.025, 0.5, 0.975), type = 7, ...)

Arguments

whichpars	Which parameters to return. Either a vector with parameter names, or "all" for all parameters, or "posterior" for parameters for which a posterior is sampled.
probs	Numeric vector of probabilities with values in [0,1].
type	An integer between 1 and 9 selecting one of the nine quantile algorithms (see quantile).

Value

A named matrix with desired quantiles. For parameters that are not estimated, all quantiles give the fixed value.

Author(s)

Don Klinkenberg [e-mail]

References

Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.

Examples

#First build a phybreak-object.
simulation <- sim_phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation)
MCMCstate <- burnin_phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample_phybreak(MCMCstate, nsample = 100)

quantile(MCMCstate)

donkeyshot/phybreak documentation built on Sept. 17, 2021, 9:32 p.m.