tracerer

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tracerer, ‘Tracer for R’ is an R package to work with BEAST2 output files.

tracerer logo

tracerer is part of thebabette package suite:

• beautier creates BEAST2 input (.xml) files.
• beastier runs BEAST2
• mauricer: install BEAST2 packages
• tracerer pastes BEAST2 output (.log,.trees, etc) files.

Related R packages:

• lumier: Shiny app to help create the function call needed
• BEASTmasteR: tip-dating using fossils as dated terminal taxa
• RBeast: misc other things
• tracerer_on_windows: verifiestracerer builds on Windows

Obtain an example log file its name

filename <- get_tracerer_path(“beast2_example_output.log”)

Parse that log file

beast_log_full <- parse_beast_tracelog_file(filename)

Remove the burn-in

beast_log <- remove_burn_ins( beast_log_full, burn_in_fraction = 0.1 )

Calculates the effective sample sizes of all parameter estimates

esses <- calc_esses(beast_log, sample_interval = 1000)

## InstallationYou can install: * (recommended) The CRAN version * The stable development version * The bleeding edge development version### CRAN`tracerer` is on CRAN:```{r}install.packages("tracerer")