traceplots: Create MCMC trace plots

In bitrugs: Bayesian Inference of Transmission Routes Using Genome Sequences

Description

Create MCMC trace plots for the transmission parameters

Usage

traceplots(mcmcoutput, tracecol="lightgrey", labels=c("p","z","beta","gamma",
"gamma_G","genpar"), burn=1, filter=1)

Arguments

mcmcoutput	MCMC output from the transmission_analysis function.
tracecol	Trace color.
labels	Character vector for parameter names.
burn	Burn-in length. This is not plotted.
filter	Retain every nth iteration.

Details

Red lines indicate the mean (solid) and 95% credible intervals (dashed) for each parameter.

Examples

  data(mcmcoutput)
  traceplots(mcmcoutput)

Example output

bitrugs documentation built on May 2, 2019, 8:55 a.m.