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tracerer (version 2.2.3)

Tracer from R

Description

'BEAST2' () 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' () 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.

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Install

install.packages('tracerer')

Monthly Downloads

290

Version

2.2.3

License

GPL-3

Issues

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Repository

https://docs.ropensci.org/tracerer/ (website) https://github.com/ropensci/tracerer/

Maintainer

Richel Bilderbeek

Last Published

September 27th, 2023

Functions in tracerer (2.2.3)

calc_summary_stats_traces

Calculates the Effective Sample Sizes of the traces of multiple estimated variables.

calc_summary_stats_trace

Calculates the Effective Sample Sizes of one estimated variable's trace.

extract_operators_lines

Extract the JSON lines out of a .xml.state with the unparsed BEAST2 MCMC operator acceptances file with the operators

default_params_doc

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

parse_beast_log

Deprecated function to parse a BEAST2 .log output file. Use parse_beast_tracelog_file instead

parse_beast_output_files

Parse all BEAST2 output files

parse_beast_state_operators

Parses a BEAST2 state .xml.state output file to get only the operators acceptances

get_tracerer_paths

Get the full paths of files in the inst/extdata folder

parse_beast_posterior

Parses BEAST2 output files to a posterior

Removed the burn-in from a trace

remove_burn_ins

Removed the burn-ins from a data frame

Measure if a file a valid BEAST2 .trees file

Calculate the corrected sample standard deviation.

save_beast_trees

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 R

parse_beast_tracelog_file

Parses a BEAST2 tracelog .log output file

is_trees_posterior

Determines if the input is a BEAST2 posterior, as parsed by parse_beast_trees

save_beast_estimates

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 R

parse_beast_trees

Parses a BEAST2 .trees output file

Check if the trace is a valid. Will stop if not

Determines if the input is a BEAST2 posterior

get_tracerer_tempfilename

Get a temporary filename

tracerer-package

tracerer: A package to parse BEAST2 output files.

Calculate the geometric mean

Calculates the Effective Sample Sizes from a parsed BEAST2 log file

Calculate the auto correlation time from https://github.com/beast-dev/beast-mcmc/blob/800817772033c13061f026226e41128d21fd14f3/src/dr/inference/trace/TraceCorrelation.java#L159 # nolint

Calculate the auto-correlation time, alternative implementation

calc_hpd_interval

Calculate the Highest Probability Density of an MCMC trace that has its burn-in removed

calc_stderr_mean

Calculate the standard error of the mean

calc_std_error_of_mean_cpp

Calculates the standard error of the mean

calc_summary_stats

Calculates the Effective Sample Sizes of one estimated variable's trace.

Calculate the auto-correlation time using only R. Consider using calc_act instead, as it is orders of magnitude faster

Calculates the Effective Sample Size

Calculate the mode of values If the distribution is bi or multimodal or uniform, NA is returned

count_trees_in_file

Count the number of trees in a .trees file

get_tracerer_path

Get the full path of a file in the inst/extdata folder