tracerer

Branch
`main`
`develop`

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

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:

install.packages("tracerer")

Stable development version

Install the tracerer main branch using remotes:

# remotes::install_github("ropensci/tracerer")
install.packages("tracerer", repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bleeding edge development version

Install the tracerer develop branch using remotes:

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.