{ "_id": "6a1ef244b401979e734143b2", "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": "2026-05-13 11:02:32 UTC", "RemoteUrl": "https://github.com/ropensci/tracerer", "RemoteRef": "main", "RemoteSha": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-19 07:48:27 UTC", "User": "root" }, "Author": "Richèl J.C. Bilderbeek [aut, cre] (ORCID:\n),\nJoëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,\nsee https://github.com/ropensci/onboarding/issues/209),\nRoberto Villegas-Diaz [ctb],\nDavid Winter [rev] (David reviewed the package for rOpenSci, see\nhttps://github.com/ropensci/onboarding/issues/209)", "MD5sum": "f0c2bae45e60a2e6ebb6a81c52b9c05b", "_user": "ropensci", "_type": "src", "_file": "tracerer_2.2.4.tar.gz", "_fileid": "f613903c5b5425dda4592f55a285bc5f1f88dfd2173b128a1c10c62dcb6dd49b", "_filesize": 1427296, "_sha256": "f613903c5b5425dda4592f55a285bc5f1f88dfd2173b128a1c10c62dcb6dd49b", "_created": "2026-05-19T07:48:27.000Z", "_published": "2026-06-02T15:09:56.972Z", "_distro": "noble", "_jobs": [ { "job": 79103945539, "time": 123, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7077775794" }, { "job": 79103945700, "time": 137, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7077779868" }, { "job": 79103946920, "time": 129, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7077776945" }, { "job": 79103947388, "time": 127, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7077777108" }, { "job": 79103946918, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7077773069" }, { "job": 79103946581, "time": 299, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7077830866" }, { "job": 79103946911, "time": 122, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7077774948" }, { "job": 79103946842, "time": 192, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7077797460" }, { "job": 79103945166, "time": 165, "config": "pkgdown", "r": "4.6.0", "check": "OK", "artifact": "7077732126" }, { "job": 79103945633, "time": 181, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7077736662" }, { "job": 79103944964, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7361731413" }, { "job": 79103945795, "time": 148, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7077782935" }, { "job": 79103946061, "time": 98, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7077768134" }, { "job": 79103945867, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7077768796" } ], "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ropensci/tracerer", "_commit": { "id": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "author": "richelbilderbeek ", "committer": "richelbilderbeek ", "message": "Install libglpk-dev\n", "time": 1778670152 }, "_maintainer": { "name": "Richèl J.C. Bilderbeek", "email": "rjcbilderbeek@gmail.com", "login": "richelbilderbeek", "orcid": "0000-0003-1107-7049", "description": "Thinks Open Science is a pleonasm.\nIn my free time, I teach programming and lead programming teams, both for/with kids and adults.", "uuid": 2098230 }, "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "jsonlite", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "phangorn", "role": "Suggests" }, { "package": "rappdirs", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-39", "n": 2 }, { "week": "2025-44", "n": 1 }, { "week": "2026-09", "n": 3 }, { "week": "2026-11", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-20", "n": 1 } ], "_tags": [], "_stars": 8, "_contributors": [ { "user": "richelbilderbeek", "count": 15, "uuid": 2098230 }, { "user": "olivroy", "count": 10, "uuid": 52606734 }, { "user": "villegar", "count": 3, "uuid": 5126692 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 319, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tracerer" }, "_mentions": 1, "_devurl": "https://github.com/ropensci/tracerer", "_pkgdown": "https://docs.ropensci.org/tracerer/", "_searchresults": 80, "_topics": [ "cpp" ], "_metadata": { "ropensci_category": "scalereprod" }, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/tracerer.html", "manual.pdf" ], "_homeurl": "https://github.com/ropensci/tracerer", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "1.5.1", "date": "2018-10-30" }, { "version": "2.0.1", "date": "2019-03-04" }, { "version": "2.0.2", "date": "2019-12-02" }, { "version": "2.1", "date": "2020-05-06" }, { "version": "2.2.2", "date": "2021-05-30" }, { "version": "2.2.3", "date": "2023-09-27" }, { "version": "2.2.4", "date": "2026-03-02" } ], "_exports": [ "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 # 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" ] } ], "_readme": "https://github.com/ropensci/tracerer/raw/main/README.md", "_rundeps": [ "jsonlite", "Rcpp" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "demo.Rmd", "filename": "demo.html", "title": "tracerer versus Tracer demo", "author": "Richèl J.C. Bilderbeek", "engine": "knitr::rmarkdown", "headings": [], "created": "2018-02-01 13:20:15", "modified": "2021-05-14 07:19:37", "commits": 16 } ], "_score": 7.538573733806856, "_indexed": true, "_nocasepkg": "tracerer", "_universes": [ "ropensci", "richelbilderbeek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.4", "date": "2026-05-19T07:50:39.000Z", "distro": "noble", "arch": "aarch64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "8c83cef3106dc2656901f45aa02b63c2c8d372514dbe72d76b123fe8f99b378a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.7.0", "os": "linux", "version": "2.2.4", "date": "2026-05-19T07:50:48.000Z", "distro": "noble", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "683aaf860767ad30ddd5f029c808400c4a82148fa45b75ad1f7178ac1f99b4ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "linux", "version": "2.2.4", "date": "2026-05-19T07:50:44.000Z", "distro": "noble", "arch": "aarch64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "58d848c4dbbbd174e30ee66d12b1abdd6a9d0f716e0b637976679cbe5fa8e149", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "linux", "version": "2.2.4", "date": "2026-05-19T07:50:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "c1fe0718ac5735e66315be36243461477ebdeb530e09c74a92b22147ff602f8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.5.3", "os": "mac", "version": "2.2.4", "date": "2026-05-19T07:50:24.000Z", "arch": "aarch64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "d41898af80c5d0d79e7b00ded726c7df8ab8d587395e2ec1913fd420fe38c06c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.5.3", "os": "mac", "version": "2.2.4", "date": "2026-05-19T07:52:43.000Z", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "be44db4f23a5226eac52565cdff0a1fbdebf5160ddf6a1322d1f3388d881402b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "mac", "version": "2.2.4", "date": "2026-05-19T07:50:29.000Z", "arch": "aarch64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "cb423562fa972fefb36d81d340161e8af4f1a47d2baf0ca4832980460c8aa9ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "mac", "version": "2.2.4", "date": "2026-05-19T07:51:29.000Z", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "e81bc97c26cf97539d1ee44abaab6618581260a56abd9d0f047caf7c87db526f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.7.0", "os": "win", "version": "2.2.4", "date": "2026-05-19T07:50:15.000Z", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "574ee8f2d6e60335e2df5ef1d25f9c97b62d26f3aa966b33715f52070cb2f3f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.5.3", "os": "win", "version": "2.2.4", "date": "2026-05-19T07:49:50.000Z", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "6eff6d0448ab18b062724c119a674c77fe0c0a57dd00b32f8a53459271d3c35f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "win", "version": "2.2.4", "date": "2026-05-19T07:49:49.000Z", "arch": "x86_64", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "e974c66cd36c2a69c4fc00bc0e7fbc554361b055f3320d29c3c36086ac5b9aca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.4", "date": "2026-06-02T15:09:05.000Z", "arch": "emscripten", "commit": "31e3e09dd93b5c19de9b4f3dff79967da07543c1", "fileid": "a6885feb56047719387c782bfe118c723eb51b8a3687f223bd5b7a5a8c841833", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26083621820" } ] }