{ "_id": "6ad1fc5bc96d212026e704d0", "Package": "o2ools", "Title": "Tools for 'outbreaker2'", "Version": "0.0.1", "Authors@R": "person(\"Cyril\", \"Geismar\", email = \"c.geismar21@imperial.ac.uk\", role = c(\"aut\", \"cre\"))", "Description": "Streamlines the post-processing, summarization, and\nvisualization of 'outbreaker2' output via a suite of helper\nfunctions. Facilitates tidy manipulation of posterior samples,\nintegration with case metadata, generation of diagnostic plots\nand summary statistics.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://github.com/CyGei/o2ools, https://cygei.github.io/o2ools/", "BugReports": "https://github.com/CyGei/o2ools/issues", "Repository": "https://cygei.r-universe.dev", "Date/Publication": "2025-12-10 14:21:34 UTC", "RemoteUrl": "https://github.com/cygei/o2ools", "RemoteRef": "HEAD", "RemoteSha": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 10:25:30 UTC", "User": "root" }, "Author": "Cyril Geismar [aut, cre]", "Maintainer": "Cyril Geismar ", "_user": "cygei", "_type": "src", "_file": "o2ools_0.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/8fd06691c0a2d862a871cc52737d6639560607538f373ecc238e852169db5d4b", "_filesize": 1241698, "_sha256": "8fd06691c0a2d862a871cc52737d6639560607538f373ecc238e852169db5d4b", "_expires": "2027-01-24T10:28:41.000Z", "_created": "2026-10-16T10:25:30.000Z", "_published": "2026-10-16T10:28:43.315Z", "_buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116927614453, "time": 153, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12040720927" }, { "job": 116927614405, "time": 147, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12039789705" }, { "job": 116927614565, "time": 87, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12039794427" }, { "job": 116927614552, "time": 85, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12040925134" }, { "job": 116926235223, "time": 224, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12039896627" }, { "job": 116927614465, "time": 91, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12040081839" }, { "job": 116927615086, "time": 91, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12040650682" }, { "job": 116927614460, "time": 60, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12040420791" }, { "job": 116927614470, "time": 74, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12040855364" } ], "_upstream": "https://github.com/cygei/o2ools", "_commit": { "id": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "author": "CyGei ", "committer": "CyGei ", "message": "CRAN downloads badge\n", "time": 1765376494 }, "_maintainer": { "name": "Cyril Geismar", "email": "c.geismar21@imperial.ac.uk", "login": "cygei", "description": "Infectious disease modeller at Johns Hopkins University.\nDeveloping tools and methods for epidemic forecasting and outbreak reconstruction.", "uuid": 93768792 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "outbreaker2", "role": "Suggests" }, { "package": "incidence2", "role": "Suggests" }, { "package": "mixtree", "role": "Suggests" }, { "package": "epicontacts", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "furrr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "tidygraph", "role": "Suggests" }, { "package": "ggraph", "role": "Suggests" } ], "_owner": "cygei", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 3 }, { "week": "2025-50", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "cygei", "count": 24, "uuid": 93768792 } ], "_userbio": { "uuid": 93768792, "type": "user", "name": "Cy Geismar", "followers": 10, "description": "Infectious disease modeller at Johns Hopkins University.\r\nDeveloping tools and methods for epidemic forecasting and outbreak reconstruction." }, "_downloads": { "count": 355, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/o2ools" }, "_devurl": "https://github.com/cygei/o2ools", "_pkgdown": "https://cygei.github.io/o2ools/", "_searchresults": 11, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/o2ools.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/cygei/o2ools", "_realowner": "cygei", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2025-06-06" } ], "_exports": [ "augment_linelist", "filter_chain", "get_accuracy", "get_consensus", "get_entropy", "get_Ri", "get_si", "get_trees", "identify", "sample.outbreaker_chains", "ttable" ], "_datasets": [ { "name": "linelist", "title": "Simulated linelist with group labels", "object": "linelist", "class": [ "data.frame" ], "fields": [ "id", "name", "group", "onset", "sample" ], "rows": 30, "table": true, "tojson": true }, { "name": "out", "title": "outbreaker2 toy dataset", "object": "out", "class": [ "outbreaker_chains", "data.frame" ], "fields": [ "step", "post", "like", "prior", "mu", "pi", "eps", "lambda", "alpha_1", "alpha_2", "alpha_3", "alpha_4", "alpha_5", "alpha_6", "alpha_7", "alpha_8", "alpha_9", "alpha_10", "alpha_11", "alpha_12", "alpha_13", "alpha_14", "alpha_15", "alpha_16", "alpha_17", "alpha_18", "alpha_19", "alpha_20", "alpha_21", "alpha_22", "alpha_23", "alpha_24", "alpha_25", "alpha_26", "alpha_27", "alpha_28", "alpha_29", "alpha_30", "t_inf_1", "t_inf_2", "t_inf_3", "t_inf_4", "t_inf_5", "t_inf_6", "t_inf_7", "t_inf_8", "t_inf_9", "t_inf_10", "t_inf_11", "t_inf_12", "t_inf_13", "t_inf_14", "t_inf_15", "t_inf_16", "t_inf_17", "t_inf_18", "t_inf_19", "t_inf_20", "t_inf_21", "t_inf_22", "t_inf_23", "t_inf_24", "t_inf_25", "t_inf_26", "t_inf_27", "t_inf_28", "t_inf_29", "t_inf_30", "kappa_1", "kappa_2", "kappa_3", "kappa_4", "kappa_5", "kappa_6", "kappa_7", "kappa_8", "kappa_9", "kappa_10", "kappa_11", "kappa_12", "kappa_13", "kappa_14", "kappa_15", "kappa_16", "kappa_17", "kappa_18", "kappa_19", "kappa_20", "kappa_21", "kappa_22", "kappa_23", "kappa_24", "kappa_25", "kappa_26", "kappa_27", "kappa_28", "kappa_29", "kappa_30" ], "rows": 201, "table": true, "tojson": true } ], "_help": [ { "page": "augment_linelist", "title": "Append summaries of outbreaker results to a linelist", "topics": [ "augment_linelist" ] }, { "page": "filter_chain", "title": "Filter chain by parameter threshold", "topics": [ "filter_chain" ] }, { "page": "get_accuracy", "title": "Calculate the accuracy of outbreak reconstruction", "topics": [ "get_accuracy" ] }, { "page": "get_consensus", "title": "Get the consensus transmission tree", "topics": [ "get_consensus" ] }, { "page": "get_entropy", "title": "Compute the entropy of transmission trees", "topics": [ "get_entropy" ] }, { "page": "get_Ri", "title": "Compute case reproduction numbers (Ri) from outbreaker2 chains", "topics": [ "get_Ri" ] }, { "page": "get_si", "title": "Compute the serial interval (si) from transmission trees", "topics": [ "get_si" ] }, { "page": "get_trees", "title": "Extract posterior transmission trees", "topics": [ "get_trees" ] }, { "page": "identify", "title": "Replace integers in outbreaker2 output with unique identifiers", "topics": [ "identify" ] }, { "page": "linelist", "title": "Simulated linelist with group labels", "topics": [ "linelist" ] }, { "page": "out", "title": "outbreaker2 toy dataset", "topics": [ "out" ] }, { "page": "sample.outbreaker_chains", "title": "Sample rows from an outbreaker_chains object", "topics": [ "sample.outbreaker_chains" ] }, { "page": "ttable", "title": "Compute the transmission contingency table", "topics": [ "ttable" ] } ], "_pkglogo": "https://github.com/cygei/o2ools/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cygei/o2ools/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "o2ools.Rmd", "filename": "o2ools.html", "title": "Processing the output of outbreaker2 with o2ools", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Identify", "Get individual trees", "Performance", "Accuracy", "Entropy", "Visualisation", "Augment the linelist with outbreaker2's results", "Consensus tree", "Maximum posterior tree", "Additional analyses" ], "created": "2025-05-07 18:08:44", "modified": "2025-06-03 13:33:28", "commits": 2 } ], "_score": 4.041392685158225, "_indexed": true, "_nocasepkg": "o2ools", "_universes": [ "cygei" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.1", "date": "2026-10-16T10:28:02.000Z", "distro": "resolute", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/1e741cf5010a56bd5d0c18392e97f3f8a0c496b81ba76c1a4fdfb47a67796c2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.6.1", "os": "linux", "version": "0.0.1", "date": "2026-10-16T10:27:57.000Z", "distro": "resolute", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/46008cc7c51f2898d93bca089d102430177756fd4b6cd15dae8e907e68e0d2c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.5.3", "os": "mac", "version": "0.0.1", "date": "2026-10-16T10:27:07.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/f32f4bd3319f4cbed56791022244b313f2dea96f4d5f04733274f2b952914a00", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.6.1", "os": "mac", "version": "0.0.1", "date": "2026-10-16T10:27:05.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/f78e02c04e1bc47be4727a06ed2300b3209d606255ce074e021ec4f6be3663e6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.1", "date": "2026-10-16T10:27:18.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/0e335042dc67d0142bbb5e166a68a9fbc9bffcfe7cd41e0aa9eaa6e754a43e29", "status": "success", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.7.0", "os": "win", "version": "0.0.1", "date": "2026-10-16T10:26:58.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/333e9c8f0d4d2965a5fec23c67c462e224cc09a104565a62c96553bc81479595", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.5.3", "os": "win", "version": "0.0.1", "date": "2026-10-16T10:26:33.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/0e8efa2fab759cb2cae7b18d4da568c767a95d3155a89f132dc3c960d397c6b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" }, { "r": "4.6.1", "os": "win", "version": "0.0.1", "date": "2026-10-16T10:26:42.000Z", "commit": "3e6bc15ce7c2a85f8d20c91f0d67cf6e56b6f97c", "fileid": "https://r2.ropensci.org/f66d815bfe2007269a753ae0d9479c72f9499a57a94128effdab16a92c4813fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cygei/actions/runs/38886718587" } ] }