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]

tracerer_2.2.3.tar.gz
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tracerer.pdf |tracerer.html✨
tracerer/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

6.43 score 8 stars 3 packages 75 scripts 228 downloads 1 mentions 31 exports 3 dependencies

Last updated 1 years agofrom:82c8d826a0. Checks:OK: 4 NOTE: 5. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64NOTENov 05 2024
R-4.5-linux-x86_64NOTENov 05 2024
R-4.4-win-x86_64NOTENov 05 2024
R-4.4-mac-x86_64NOTENov 05 2024
R-4.4-mac-aarch64NOTENov 05 2024
R-4.3-win-x86_64OKNov 05 2024
R-4.3-mac-x86_64OKNov 05 2024
R-4.3-mac-aarch64OKNov 05 2024

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 Nov 05 2024.

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

Readme and manuals

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