{ "_id": "6a1a73ed1d7bb097a09d12c4", "Package": "treeducken", "Type": "Package", "Title": "Nested Phylogenetic Tree Simulator", "Version": "1.1.0.9999", "Authors@R": "c(person(\"Wade\", \"Dismukes\", email=\"wade.dismukes@gmail.com\",\nrole=c(\"aut\",\"cre\")),\nperson(c(\"Tracy\",\"A.\"), \"Heath\", role=c(\"aut\")),\nperson(\"Josh\", \"Justison\", role=c(\"ctb\")),\nperson(\"Damien\", \"de Vienne\", role=c(\"ctb\")),\nperson(\"Liam\", \"Revell\", role=c(\"ctb\")),\nperson(\"Emmanuel\", \"Paradis\", role=c(\"ctb\")),\nperson(\"Klaus\", \"Schliep\", role=c(\"ctb\")),\nperson(\"Ben\", \"Bolker\", role=c(\"ctb\")),\nperson(c(\"Luke\",\"J.\"), \"Harmon\", role=c(\"ctb\")),\nperson(c(\"Joseph\",\"W.\"), \"Brown\", role=c(\"ctb\")))", "Description": "Simulates nested phylogenetic trees (gene trees in species\ntree, symbiont trees in host trees) using birth-death processes\nand transfers between lineages. Simulations of gene trees\nwithin species trees are performed using a three-tree model\nwith species trees, locus trees, and gene trees. The\ncophylogenetic birth-death process is used to simulate sets of\nhost and symbiont trees with extant associations between tips.\nFor more information about the three-tree model see: Mallo et\nal. (2015) , Rasmussen and Kellis\n(2012) .", "License": "GPL-3", "SystemRequirements": "C++11", "RoxygenNote": "7.1.1", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2023-03-19 16:35:31 UTC", "RemoteUrl": "https://github.com/wadedismukes/treeducken", "RemoteRef": "HEAD", "RemoteSha": "032b92e3b4294f960854a0b497f6f87330db63ee", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 06:01:47 UTC", "User": "root" }, "Author": "Wade Dismukes [aut, cre],\nTracy A. Heath [aut],\nJosh Justison [ctb],\nDamien de Vienne [ctb],\nLiam Revell [ctb],\nEmmanuel Paradis [ctb],\nKlaus Schliep [ctb],\nBen Bolker [ctb],\nLuke J. Harmon [ctb],\nJoseph W. 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"topics": [ "build_historical_association_matrix", "get_assoc" ] }, { "page": "c.cophy", "title": "Combine cophylogenetic sets into a multiCophy object", "topics": [ "c.cophy", "c.multiCophy" ] }, { "page": "calculate_expected_leaves_locustree", "title": "Calculate expected leaves of a locus tree", "topics": [ "ave_tips_lt", "calculate_expected_leaves_locustree" ] }, { "page": "calculate_expected_leaves_sptree", "title": "Calculate expected leaves of a species tree", "topics": [ "ave_tips_st", "calculate_expected_leaves_sptree" ] }, { "page": "collapse_locus_subtree", "title": "Collapse a clade into a single tip", "topics": [ "collapse_clade", "collapse_locus_subtree" ] }, { "page": "convert_assoc_table_to_matrix", "title": "Convert a table with host and symbiont associations to a matrix", "topics": [ "convert_assoc_table_to_matrix", "make_mat" ] }, { "page": "convert_to_cophy", "title": "Converts an object into an object of type cophy", "topics": [ "convert_to_cophy", "to_cophy" ] }, { "page": "cophy_summary_stat", "title": "Calculates summary statistics for cophylogenetic objects", "topics": [ "cophy_summary_stat", "cophy_summary_stat_by_indx", "summarize_1cophy", "summarize_cophy" ] }, { "page": "count_cherries", "title": "Calculate cherry statistic for gene-trees", "topics": [ "count_cherries" ] }, { "page": "draw_cophy", "title": "Internal tree plot function", "topics": [ "draw_cophy" ] }, { "page": "draw_curve", "title": "Curve draw function", "topics": [ "draw_curve" ] }, { "page": "drop_extinct", "title": "Drops extinct tips from tree", "topics": [ "drop_extinct" ] }, { "page": "estimate_node_heights", "title": "Calculate expected time to branching point of a species tree", "topics": [ "estimate_node_heights", "node_heights" ] }, { "page": "summary.cophy", "title": "Summarize a cophylogenetic set", "topics": [ "event_history", "event_history.cophy", "summary.cophy" ] }, { "page": "genetree_summary_stat", "title": "Calculate summary statistics for gene trees", "topics": [ "genetree_summary_stat", "summarize_gt" ] }, { "page": "get_loci", "title": "Separate a locus tree into loci", "topics": [ "get_loci" ] }, { "page": "get_tip_labels_tree_list", "title": "Get all the tip labels of a `multiPhylo` object", "topics": [ "get_tipnames", "get_tip_labels_tree_list" ] }, { "page": "print.cophy", "title": "Print a cophylogenetic set", "topics": [ "association_mat", "association_mat.cophy", "association_mat.multiCophy", "event_history.multiCophy", "host_tree", "host_tree.cophy", "host_tree.multiCophy", "print.cophy", "print.multiCophy", "symb_tree", "symb_tree.cophy", "symb_tree.multiCophy" ] }, { "page": "is_extinct", "title": "Identify extinct tips from tree", "topics": [ "is_extinct" ] }, { "page": "is.cophy", "title": "Test for the cophylogenetic set object", "topics": [ "is.cophy", "is.multiCophylo" ] }, { "page": "make_textbox", "title": "Internal tree plot function", "topics": [ "make_textbox" ] }, { "page": "parafit_stat", "title": 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