README.md

In richelbilderbeek/tracerer: Tracer from R

tracerer

Branch || ---------|-----------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------- master | | develop| |

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

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 master branch using remotes:

remotes::install_github("ropensci/tracerer")

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

• BEAST2 GitHub repository
• Tracer GitHub repository

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.

richelbilderbeek/tracerer documentation built on Oct. 2, 2023, 7:32 a.m.