# Tracer from R

## Documentation for package ‘tracerer’ version 2.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

calc_act | Calculate the auto-correlation time, alternative implementation
calc_act_cpp | Calculate the auto correlation time from <URL: 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_geom_mean | Calculate the geometric mean
calc_hpd_interval | Calculate the Highest Probability Density of an MCMC trace that has its burn-in removed
calc_mode | Calculate the mode of values If the distribution is bi or multimodal or uniform, NA is returned
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.
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.
check_trace | Check if the trace is a valid. Will stop if not
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
get_tracerer_tempfilename | Get a temporary filename
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 | 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_posterior | Parses BEAST2 output files to a posterior
parse_beast_state_operators | Parses a BEAST2 state '.xml.state' output file to get only the operators acceptances
parse_beast_tracelog_file | Parses a BEAST2 tracelog '.log' output file
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.