knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
tracerer
: 'Tracer for R' is an R package that does the same as
Tracer does, from within R.
To use tracerer
, it needs to be loaded:
library(tracerer)
When loading beast2_example_output.log
in Tracer, the following is displayed:
Most prominently, at the left, the effective sample sizes (ESSes) are shown.
The show the ESSes using tracerer
:
estimates <- parse_beast_tracelog_file( get_tracerer_path("beast2_example_output.log") ) estimates <- remove_burn_ins(estimates, burn_in_fraction = 0.1) esses <- calc_esses(estimates, sample_interval = 1000) table <- t(esses) colnames(table) <- c("ESS") knitr::kable(table)
At the top-right, some measures of the variable posterior
is shown.
To reproduce these measures in tracerer
:
sum_stats <- calc_summary_stats( estimates$posterior, sample_interval = 1000 ) table <- t(sum_stats) colnames(table) <- c("sum_stat") knitr::kable(table)
Unlike Tracer, in tracerer
all summary statistics can be obtained at once:
sum_stats <- calc_summary_stats( estimates, sample_interval = 1000 ) knitr::kable(sum_stats)
At the bottom-right, a histogram of the posterior estimates is shown.
To reproduce these measures in tracerer
:
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))
Tracer can also show the trace of each estimated variable:
Same can be done with tracerer
:
ggplot2::ggplot( data = remove_burn_ins(estimates, burn_in_fraction = 0.1), ggplot2::aes(x = Sample) ) + ggplot2::geom_line(ggplot2::aes(y = posterior))
tracerer
can also use part of DensiTree
's functionality.
Here is beast2_example_output.trees
displayed by DensiTree
:
The same is achieved in tracerer
with:
trees <- parse_beast_trees( get_tracerer_path("beast2_example_output.trees") ) phangorn::densiTree(trees, width = 2)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.