calc_hpd_interval: Calculate the Highest Probability Density of an MCMC trace...
In tracerer: Tracer from R

Description Usage Arguments Value Author(s) See Also Examples

Calculate the Highest Probability Density of an MCMC trace that has its burn-in removed

1	calc_hpd_interval(trace, proportion = 0.95)

`trace`	a numeric vector of parameter estimates obtained from an MCMC run. Must have its burn-in removed
`proportion`	the proportion of numbers within the interval. For example, use 0.95 for a 95 percentage interval

a numeric vector, with at index 1 the lower boundary of the interval, and at index 2 the upper boundary of the interval

The original Java version of the algorithm was from J. Heled, ported to R and adapted by Richèl J.C. Bilderbeek

The function remove_burn_in removes a burn-in. The Java code that inspired this function can be found here: https://github.com/beast-dev/beast-mcmc/blob/98705c59db65e4f406a420bbade949aeecfe05d0/src/dr/stats/DiscreteStatistics.java#L317 # nolint URLs can be long

estimates <- parse_beast_tracelog_file(
  get_tracerer_path("beast2_example_output.log")
)
tree_height_trace <- remove_burn_in(
  estimates$TreeHeight,
  burn_in_fraction = 0.1
)

# Values will be 0.453 and 1.816
calc_hpd_interval(tree_height_trace, proportion = 0.95)