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_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.
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.
