{ "_id": "69eefa923c89364019f46023", "Package": "tracerer", "Type": "Package", "Title": "Tracer from R", "Version": "2.2.4", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"rjcbilderbeek@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")),\nperson(\"Joëlle\", \"Barido-Sottani\", role = \"rev\", comment = \"Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209\"),\nperson(\"Roberto\", \"Villegas-Diaz\", role = \"ctb\"),\nperson(\"David\", \"Winter\", role = \"rev\", comment = \"David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209\"))", "Maintainer": "Richèl J.C. Bilderbeek ", "Description": "'BEAST2' () is a widely used\nBayesian phylogenetic tool, that uses DNA/RNA/protein data and\nmany model priors to create a posterior of jointly estimated\nphylogenies and parameters. 'Tracer'\n() is a GUI tool to parse\nand analyze the files generated by 'BEAST2'. This package\nprovides a way to parse and analyze 'BEAST2' input files\nwithout active user input, but using R function calls instead.", "License": "GPL-3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "URL": "https://docs.ropensci.org/tracerer/ (website)\nhttps://github.com/ropensci/tracerer/", "BugReports": "https://github.com/ropensci/tracerer/issues", "Language": "en-US", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-04-27 05:31:31 UTC", "RemoteUrl": "https://github.com/ropensci/tracerer", "RemoteRef": "main", "RemoteSha": "7a34550f1b39ffe4809cc3b2f5a075629cbf8fc0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-04-27 05:52:28 UTC", "User": "root" }, "Author": "Richèl J.C. 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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. 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