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| tracerer-package | 'tracerer': A package to parse BEAST2 output files. |
| 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_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. |
| 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_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. |