demo.R
In tracerer: Tracer from R

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(tracerer)

## -----------------------------------------------------------------------------
estimates <- parse_beast_tracelog_file(
  get_tracerer_path("beast2_example_output.log")
)
estimates <- remove_burn_ins(estimates, burn_in_fraction = 0.1)
esses <- calc_esses(estimates, sample_interval = 1000)
table <- t(esses)
colnames(table) <- c("ESS")
knitr::kable(table)

## -----------------------------------------------------------------------------
sum_stats <- calc_summary_stats(
  estimates$posterior,
  sample_interval = 1000
)
table <- t(sum_stats)
colnames(table) <- c("sum_stat")
knitr::kable(table)

## -----------------------------------------------------------------------------
sum_stats <- calc_summary_stats(
  estimates,
  sample_interval = 1000
)
knitr::kable(sum_stats)

## -----------------------------------------------------------------------------
ggplot2::ggplot(
  data = remove_burn_ins(estimates, burn_in_fraction = 0.1),
  ggplot2::aes(posterior)
) + ggplot2::geom_histogram(binwidth = 0.21) +
  ggplot2::scale_x_continuous(breaks = seq(-75, -68))


## -----------------------------------------------------------------------------
ggplot2::ggplot(
  data = remove_burn_ins(estimates, burn_in_fraction = 0.1),
  ggplot2::aes(x = Sample)
) + ggplot2::geom_line(ggplot2::aes(y = posterior))


## ----fig.width=7, fig.height=7------------------------------------------------
trees <- parse_beast_trees(
  get_tracerer_path("beast2_example_output.trees")
)
phangorn::densiTree(trees, width = 2)