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      "date": "2018-10-30"
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      "date": "2019-03-04"
    },
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      "date": "2019-12-02"
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      "date": "2023-09-27"
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    "calc_act",
    "calc_act_r",
    "calc_ess",
    "calc_esses",
    "calc_geom_mean",
    "calc_hpd_interval",
    "calc_mode",
    "calc_stderr_mean",
    "calc_summary_stats",
    "calc_summary_stats_trace",
    "calc_summary_stats_traces",
    "check_trace",
    "count_trees_in_file",
    "cs_std_dev",
    "extract_operators_lines",
    "get_tracerer_path",
    "get_tracerer_paths",
    "get_tracerer_tempfilename",
    "is_posterior",
    "is_trees_file",
    "is_trees_posterior",
    "parse_beast_log",
    "parse_beast_output_files",
    "parse_beast_posterior",
    "parse_beast_state_operators",
    "parse_beast_tracelog_file",
    "parse_beast_trees",
    "remove_burn_in",
    "remove_burn_ins",
    "save_beast_estimates",
    "save_beast_trees"
  ],
  "_help": [
    {
      "page": "calc_act",
      "title": "Calculate the auto-correlation time, alternative implementation",
      "topics": [
        "calc_act"
      ]
    },
    {
      "page": "calc_act_cpp",
      "title": "Calculate the auto correlation time from <https://github.com/beast-dev/beast-mcmc/blob/800817772033c13061f026226e41128d21fd14f3/src/dr/inference/trace/TraceCorrelation.java#L159> # nolint",
      "topics": [
        "calc_act_cpp"
      ]
    },
    {
      "page": "calc_act_r",
      "title": "Calculate the auto-correlation time using only R. Consider using calc_act instead, as it is orders of magnitude faster",
      "topics": [
        "calc_act_r"
      ]
    },
    {
      "page": "calc_ess",
      "title": "Calculates the Effective Sample Size",
      "topics": [
        "calc_ess"
      ]
    },
    {
      "page": "calc_esses",
      "title": "Calculates the Effective Sample Sizes from a parsed BEAST2 log file",
      "topics": [
        "calc_esses"
      ]
    },
    {
      "page": "calc_geom_mean",
      "title": "Calculate the geometric mean",
      "topics": [
        "calc_geom_mean"
      ]
    },
    {
      "page": "calc_hpd_interval",
      "title": "Calculate the Highest Probability Density of an MCMC trace that has its burn-in removed",
      "topics": [
        "calc_hpd_interval"
      ]
    },
    {
      "page": "calc_mode",
      "title": "Calculate the mode of values If the distribution is bi or multimodal or uniform, NA is returned",
      "topics": [
        "calc_mode"
      ]
    },
    {
      "page": "calc_std_error_of_mean_cpp",
      "title": "Calculates the standard error of the mean",
      "topics": [
        "calc_std_error_of_mean_cpp"
      ]
    },
    {
      "page": "calc_stderr_mean",
      "title": "Calculate the standard error of the mean",
      "topics": [
        "calc_stderr_mean"
      ]
    },
    {
      "page": "calc_summary_stats",
      "title": "Calculates the Effective Sample Sizes of one estimated variable's trace",
      "topics": [
        "calc_summary_stats"
      ]
    },
    {
      "page": "calc_summary_stats_trace",
      "title": "Calculates the Effective Sample Sizes of one estimated variable's trace",
      "topics": [
        "calc_summary_stats_trace"
      ]
    },
    {
      "page": "calc_summary_stats_traces",
      "title": "Calculates the Effective Sample Sizes of the traces of multiple estimated variables",
      "topics": [
        "calc_summary_stats_traces"
      ]
    },
    {
      "page": "check_trace",
      "title": "Check if the trace is a valid. Will stop if not",
      "topics": [
        "check_trace"
      ]
    },
    {
      "page": "count_trees_in_file",
      "title": "Count the number of trees in a '.trees' file",
      "topics": [
        "count_trees_in_file"
      ]
    },
    {
      "page": "cs_std_dev",
      "title": "Calculate the corrected sample standard deviation",
      "topics": [
        "cs_std_dev"
      ]
    },
    {
      "page": "default_params_doc",
      "title": "Documentation of general function arguments",
      "topics": [
        "default_params_doc"
      ]
    },
    {
      "page": "extract_operators_lines",
      "title": "Extract the JSON lines out of a '.xml.state' with the unparsed BEAST2 MCMC operator acceptances file with the operators",
      "topics": [
        "extract_operators_lines"
      ]
    },
    {
      "page": "get_tracerer_path",
      "title": "Get the full path of a file in the 'inst/extdata' folder",
      "topics": [
        "get_tracerer_path"
      ]
    },
    {
      "page": "get_tracerer_paths",
      "title": "Get the full paths of files in the 'inst/extdata' folder",
      "topics": [
        "get_tracerer_paths"
      ]
    },
    {
      "page": "get_tracerer_tempfilename",
      "title": "Get a temporary filename",
      "topics": [
        "get_tracerer_tempfilename"
      ]
    },
    {
      "page": "is_posterior",
      "title": "Determines if the input is a BEAST2 posterior",
      "topics": [
        "is_posterior"
      ]
    },
    {
      "page": "is_trees_file",
      "title": "Measure if a file a valid BEAST2 '.trees' file",
      "topics": [
        "is_trees_file"
      ]
    },
    {
      "page": "is_trees_posterior",
      "title": "Determines if the input is a BEAST2 posterior, as parsed by parse_beast_trees",
      "topics": [
        "is_trees_posterior"
      ]
    },
    {
      "page": "parse_beast_log",
      "title": "Deprecated function to parse a BEAST2 '.log' output file. Use parse_beast_tracelog_file instead",
      "topics": [
        "parse_beast_log"
      ]
    },
    {
      "page": "parse_beast_output_files",
      "title": "Parse all BEAST2 output files",
      "topics": [
        "parse_beast_output_files"
      ]
    },
    {
      "page": "parse_beast_posterior",
      "title": "Parses BEAST2 output files to a posterior",
      "topics": [
        "parse_beast_posterior"
      ]
    },
    {
      "page": "parse_beast_state_operators",
      "title": "Parses a BEAST2 state '.xml.state' output file to get only the operators acceptances",
      "topics": [
        "parse_beast_state_operators"
      ]
    },
    {
      "page": "parse_beast_tracelog_file",
      "title": "Parses a BEAST2 tracelog '.log' output file",
      "topics": [
        "parse_beast_tracelog_file"
      ]
    },
    {
      "page": "parse_beast_trees",
      "title": "Parses a BEAST2 .trees output file",
      "topics": [
        "parse_beast_trees"
      ]
    },
    {
      "page": "remove_burn_in",
      "title": "Removed the burn-in from a trace",
      "topics": [
        "remove_burn_in"
      ]
    },
    {
      "page": "remove_burn_ins",
      "title": "Removed the burn-ins from a data frame",
      "topics": [
        "remove_burn_ins"
      ]
    },
    {
      "page": "save_beast_estimates",
      "title": "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",
      "topics": [
        "save_beast_estimates"
      ]
    },
    {
      "page": "save_beast_trees",
      "title": "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",
      "topics": [
        "save_beast_trees"
      ]
    }
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  "_readme": "https://github.com/ropensci/tracerer/raw/main/README.md",
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      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
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