Package: tracerer 2.2.3

Richèl J.C. Bilderbeek

tracerer: Tracer from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev], David Winter [rev]

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tracerer.pdf |tracerer.html✨
tracerer/json (API)
NEWS

# Install 'tracerer' in R:
install.packages('tracerer', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/tracerer/issues0 issues

Pkgdown site:https://docs.ropensci.org

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:tracerer-2.2.3(2023-09-27)

Conda:

cpp

6.49 score 8 stars 3 packages 86 scripts 305 downloads 1 mentions 31 exports 3 dependencies

Last updated 1 years agofrom:82c8d826a0 (on main). Checks:4 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 25 2025
R-4.5-win-x86_64NOTEFeb 25 2025
R-4.5-mac-x86_64NOTEFeb 25 2025
R-4.5-mac-aarch64NOTEFeb 25 2025
R-4.5-linux-x86_64NOTEFeb 25 2025
R-4.4-win-x86_64NOTEFeb 25 2025
R-4.4-mac-x86_64NOTEFeb 25 2025
R-4.4-mac-aarch64NOTEFeb 25 2025
R-4.3-win-x86_64OKFeb 25 2025
R-4.3-mac-x86_64OKFeb 25 2025
R-4.3-mac-aarch64OKFeb 25 2025

Exports:calc_actcalc_act_rcalc_esscalc_essescalc_geom_meancalc_hpd_intervalcalc_modecalc_stderr_meancalc_summary_statscalc_summary_stats_tracecalc_summary_stats_tracescheck_tracecount_trees_in_filecs_std_devextract_operators_linesget_tracerer_pathget_tracerer_pathsget_tracerer_tempfilenameis_posterioris_trees_fileis_trees_posteriorparse_beast_logparse_beast_output_filesparse_beast_posteriorparse_beast_state_operatorsparse_beast_tracelog_fileparse_beast_treesremove_burn_inremove_burn_inssave_beast_estimatessave_beast_trees

Dependencies:jsonliteRcpptestit

tracerer versus Tracer demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Feb 25 2025.

Last update: 2021-05-14
Started: 2018-02-01

Citation

Bilderbeek RJ, Etienne RS (2008). “babette: BEAUti 2, BEAST 2 and Tracer for R.” Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13032.

Corresponding BibTeX entry: 

  @Article{,
    author = {Richèl JC Bilderbeek and Rampal S Etienne},
    title = {babette: BEAUti 2, BEAST 2 and Tracer for R},
    journal = {Methods in Ecology and Evolution},
    year = {2008},
    url = {https://doi.org/10.1111/2041-210X.13032},
  }

Readme and manuals

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 the babette package suite:

Related R packages:

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")
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:

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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Help Manual

Help pageTopics
Calculate the auto-correlation time, alternative implementationcalc_act
Calculate the auto correlation time from <https://github.com/beast-dev/beast-mcmc/blob/800817772033c13061f026226e41128d21fd14f3/src/dr/inference/trace/TraceCorrelation.java#L159> # nolintcalc_act_cpp
Calculate the auto-correlation time using only R. Consider using calc_act instead, as it is orders of magnitude fastercalc_act_r
Calculates the Effective Sample Sizecalc_ess
Calculates the Effective Sample Sizes from a parsed BEAST2 log filecalc_esses
Calculate the geometric meancalc_geom_mean
Calculate the Highest Probability Density of an MCMC trace that has its burn-in removedcalc_hpd_interval
Calculate the mode of values If the distribution is bi or multimodal or uniform, NA is returnedcalc_mode
Calculates the standard error of the meancalc_std_error_of_mean_cpp
Calculate the standard error of the meancalc_stderr_mean
Calculates the Effective Sample Sizes of one estimated variable's trace.calc_summary_stats
Calculates the Effective Sample Sizes of one estimated variable's trace.calc_summary_stats_trace
Calculates the Effective Sample Sizes of the traces of multiple estimated variables.calc_summary_stats_traces
Check if the trace is a valid. Will stop if notcheck_trace
Count the number of trees in a '.trees' filecount_trees_in_file
Calculate the corrected sample standard deviation.cs_std_dev
Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.default_params_doc
Extract the JSON lines out of a '.xml.state' with the unparsed BEAST2 MCMC operator acceptances file with the operatorsextract_operators_lines
Get the full path of a file in the 'inst/extdata' folderget_tracerer_path
Get the full paths of files in the 'inst/extdata' folderget_tracerer_paths
Get a temporary filenameget_tracerer_tempfilename
Determines if the input is a BEAST2 posterioris_posterior
Measure if a file a valid BEAST2 '.trees' fileis_trees_file
Determines if the input is a BEAST2 posterior, as parsed by parse_beast_treesis_trees_posterior
Deprecated function to parse a BEAST2 '.log' output file. Use parse_beast_tracelog_file insteadparse_beast_log
Parse all BEAST2 output filesparse_beast_output_files
Parses BEAST2 output files to a posteriorparse_beast_posterior
Parses a BEAST2 state '.xml.state' output file to get only the operators acceptancesparse_beast_state_operators
Parses a BEAST2 tracelog '.log' output fileparse_beast_tracelog_file
Parses a BEAST2 .trees output fileparse_beast_trees
Removed the burn-in from a traceremove_burn_in
Removed the burn-ins from a data frameremove_burn_ins
Save the BEAST2 estimates as a BEAST2 '.log' file. There will be some differences: a BEAST2 '.log' file also saves the model as comments and formats the numbers in a way non-standard to Rsave_beast_estimates
Save the BEAST2 trees as a BEAST2 '.log' file. There will be some differences: a BEAST2 '.log' file also saves the model as comments and formats the numbers in a way non-standard to Rsave_beast_trees