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

Source:`R/calc_hpd_interval.R`

`calc_hpd_interval.Rd`

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

## Arguments

- 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

## Value

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

## See also

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

## Author

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

## Examples

```
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)
#> [1] 0.4529637 1.8159958
```