All functions

calc_act()

Calculate the auto-correlation time, alternative implementation

calc_act_cpp()

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

calc_act_r()

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

calc_ess()

Calculates the Effective Sample Size

calc_esses()

Calculates the Effective Sample Sizes from a parsed BEAST2 log file

calc_hpd_interval()

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

calc_std_error_of_mean_cpp()

Calculates the standard error of the mean

calc_stderr_mean()

Calculate the standard error of the mean

calc_summary_stats()

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

calc_summary_stats_trace()

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

calc_summary_stats_traces()

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

count_trees_in_file()

Count the number of trees in a .trees file

cs_std_dev()

Calculate the corrected sample standard deviation.

default_params_doc()

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

extract_operators_lines()

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

get_tracerer_path()

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

get_tracerer_paths()

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

is_posterior()

Determines if the input is a BEAST2 posterior

is_trees_file()

Measure if a file a valid BEAST2 .trees file

is_trees_posterior()

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

parse_beast_log()

Parses a BEAST2 .log output file

parse_beast_output_files()

Parse all BEAST2 output files

parse_beast_posterior()

Parses BEAST2 output files to a posterior

parse_beast_state_operators()

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

parse_beast_trees()

Parses a BEAST2 .trees output file

remove_burn_in()

Removed the burn-in from a trace

remove_burn_ins()

Removed the burn-ins from a data frame

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

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

tracerer

tracerer: A package to parse BEAST2 output files.