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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:
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)| ESS | |
|---|---|
| posterior | 10 |
| likelihood | 10 |
| prior | 10 |
| treeLikelihood | 10 |
| TreeHeight | 7 |
| BirthDeath | 10 |
| birthRate2 | 9 |
| relativeDeathRate2 | 6 |
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)| sum_stat | |
|---|---|
| mean | -70.58394 |
| stderr_mean | 0.5044887 |
| stdev | 1.681629 |
| variance | 2.827876 |
| median | -69.87976 |
| mode | n/a |
| geom_mean | n/a |
| hpd_interval_low | -74.15268 |
| hpd_interval_high | -68.68523 |
| act | 1000 |
| ess | 10 |
Unlike Tracer, in tracerer all summary statistics can be
obtained at once:
| mean | stderr_mean | stdev | variance | median | mode | geom_mean | hpd_interval_low | hpd_interval_high | act | ess | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| posterior | -70.5839432 | 0.5044887 | 1.6816291 | 2.8278764 | -69.8797613 | n/a | n/a | -74.1526820 | -68.6852294 | 1000.000 | 10.000000 |
| likelihood | -60.1725009 | 0.3964208 | 1.3214025 | 1.7461047 | -60.0504225 | n/a | n/a | -62.4090389 | -58.7371284 | 1000.000 | 10.000000 |
| prior | -10.4114423 | 0.5424505 | 1.8081684 | 3.2694729 | -10.5950270 | n/a | n/a | -14.1703653 | -7.2820933 | 1000.000 | 10.000000 |
| treeLikelihood | -60.1725009 | 0.3964208 | 1.3214025 | 1.7461047 | -60.0504225 | n/a | n/a | -62.4090389 | -58.7371284 | 1000.000 | 10.000000 |
| TreeHeight | 0.9744748 | 0.1439937 | 0.3916244 | 0.1533697 | 0.8755907 | n/a | 0.91041547166058 | 0.4529637 | 1.8159958 | 1502.121 | 6.657254 |
| BirthDeath | -3.5036870 | 0.5424505 | 1.8081684 | 3.2694729 | -3.6872718 | n/a | n/a | -7.2626100 | -0.3743380 | 1000.000 | 10.000000 |
| birthRate2 | 1.4470488 | 0.2134411 | 0.6713951 | 0.4507714 | 1.4118781 | n/a | 1.28823302868404 | 0.3909076 | 2.8041208 | 1122.942 | 8.905181 |
| relativeDeathRate2 | 0.4937568 | 0.0650235 | 0.1709096 | 0.0292101 | 0.4480670 | n/a | 0.466468860930895 | 0.2496224 | 0.7107459 | 1608.296 | 6.217762 |
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)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.