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

tracerer logo

tracerer is part of the babette 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: verifies tracerer builds on Windows

Example

```{r} library(tracerer)

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)


## Installation

You can install:

 * (recommended) The CRAN version
 * The stable development version
 * The bleeding edge development version

### CRAN

`tracerer` is on CRAN:

```{r}
install.packages("tracerer")

Stable development version

Install the tracerer master branch using remotes:

{r} remotes::install_github("ropensci/tracerer")

Bleeding edge development version

Install the tracerer develop branch using remotes:

{r} remotes::install_github("ropensci/tracerer", ref = "develop")

FAQ

See FAQ

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at ‘Submitting code’

I think I have found a bug

See CONTRIBUTING, at ‘Submitting bugs’

There’s something else I want to say

Sure, just add an Issue. Or send an email.

External links

References

Article about babette:

Bilderbeek, Richèl JC, and Rampal S. Etienne. “babette: BEAUti 2, BEAST 2 and Tracer for R.” Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

FASTA files anthus_aco.fas and anthus_nd2.fas from:

Van Els, Paul, and Heraldo V. Norambuena. “A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data.” Ibis.

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