{ "_id": "6a180cc8acfb0bcc41dadd4f", "Package": "MSCquartets", "Type": "Package", "Title": "Analyzing Gene Tree Quartets under the Multi-Species Coalescent", "Version": "3.3", "Authors@R": "c(\nperson(\"Elizabeth\", \"Allman\", email = \"esallman@alaska.edu\",\nrole = \"aut\"),\nperson(\"Hector\", \"Banos\", email = \"hbassnos@gmail.com\",\nrole = \"aut\"),\nperson(\"Jonathan\", \"Mitchell\", email = \"jonathanmitchell88@gmail.com\",\nrole = \"aut\"),\nperson(\"Kristina\", \"Wicke\", email = \"kristina.wicke@njit.edu\",\nrole = \"aut\"),\nperson(\"John\", \"Rhodes\", email = \"j.rhodes@alaska.edu\",\nrole = c(\"aut\", \"cre\"),comment=c(ORCID = \"0000-0001-9921-1091\")) )", "Description": "Methods for analyzing and using quartets displayed on a\ncollection of gene trees, primarily to make inferences about\nthe species tree or network under the multi-species coalescent\nmodel. These include quartet hypothesis tests for the model, as\ndeveloped by Mitchell et al. (2019) ,\nsimplex plots of quartet concordance factors as presented by\nAllman et al. (2020) , species\ntree inference methods based on quartet distances of Rhodes\n(2019) and Yourdkhani and\nRhodes (2019) , the NANUQ\nalgorithm for inference of level-1 species networks of Allman\net al. (2019) , the TINNIK\nalgorithm for inference of the tree of blobs of an arbitrary\nnetwork of Allman et al.(2022)\n, NANUQ+ routines for resolving\nmultifurcations in the tree of blobs to cycles as in Rhodes et\nal.(2024) , and the ECToBlob\nalgorithm for inference of a network with no anomalous quartets\nof Allman et al. (2026) (forthcoming). Software announcement by\nRhodes et al. (2020) .", "License": "MIT + file LICENSE", "RdMacros": "Rdpack", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 09:28:50 UTC", "User": "root" }, "Author": "Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell\n[aut], Kristina Wicke [aut], John Rhodes [aut, cre] (ORCID:\n)", "Maintainer": "John Rhodes ", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://johnarhodes.r-universe.dev", "Date/Publication": "2026-05-28 08:55:23 UTC", "RemoteUrl": "https://github.com/cran/MSCquartets", "RemoteRef": "HEAD", "RemoteSha": "0b3cfb335de347e9268491c56d0a14631cacffa0", "MD5sum": "452693fe9b2d90c9db80678e29253967", "_user": "johnarhodes", "_type": "src", "_file": "MSCquartets_3.3.tar.gz", "_fileid": "149072183f76fab52e544b90c5306969774cefa3485737ca1777a55fdfc1cc1f", "_filesize": 7012787, "_sha256": 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"page": "circHybOrders", "title": "Generate all circular orders with designated hybrid", "topics": [ "circHybOrders" ] }, { "page": "collapseEdges", "title": "Collapse short tree edges", "topics": [ "collapseEdges" ] }, { "page": "combineCycleResolutions", "title": "Combine several cycle resolutions on a tree of blobs to create a network", "topics": [ "combineCycleResolutions" ] }, { "page": "combineP", "title": "Combine p-values of tests", "topics": [ "combineP" ] }, { "page": "compatibleSplits", "title": "Extract compatible splits", "topics": [ "compatibleSplits" ] }, { "page": "cutDensity", "title": "Probability density function for Cut Model", "topics": [ "cutDensity" ] }, { "page": "dataGeneTreeSample", "title": "Simulated gene tree dataset from species tree", "topics": [ "dataGeneTreeSample" ] }, { "page": "dataPapioniniVanderpool", "title": "Papionini gene tree dataset", "topics": [ "dataPapioniniVanderpool" ] }, { "page": "dataYeastRokas", "title": "Yeast gene tree dataset", 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