{ "_id": "6a227797cd65a98ecbd4bed1", "Package": "Claddis", "Type": "Package", "Title": "Measuring Morphological Diversity and Evolutionary Tempo", "Version": "0.7.0", "Date": "2024-09-01", "Authors@R": "c(\nperson(given = \"Graeme T.\", family = \"Lloyd\",\nemail = \"graemetlloyd@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(given = \"Thomas\", family = \"Guillerme\", role = c(\"aut\", \"cph\")),\nperson(given = \"Jen\", family = \"Hoyal Cuthill\", role = c(\"aut\", \"cph\")),\nperson(given = \"Emma\", family = \"Sherratt\", role = c(\"aut\", \"cph\")),\nperson(given = \"Steve C.\", family = \"Wang\", role = c(\"aut\", \"cph\"))\n)", "Maintainer": "Graeme T. Lloyd ", "Description": "Measures morphological diversity from discrete character\ndata and estimates evolutionary tempo on phylogenetic trees.\nImports morphological data from #NEXUS (Maddison et al. (1997)\n) format with read_nexus_matrix(),\nand writes to both #NEXUS and TNT format (Goloboff et al.\n(2008) ). Main functions\nare test_rates(), which implements AIC and likelihood ratio\ntests for discrete character rates introduced across Lloyd et\nal. (2012) , Brusatte et\nal. (2014) , Close et al. (2015)\n, and Lloyd (2016)\n, and\ncalculate_morphological_distances(), which implements multiple\ndiscrete character distance metrics from Gower (1971)\n, Wills (1998)\n, Lloyd (2016)\n, and Hopkins and St John (2018)\n. This also includes the GED\ncorrection from Lehmann et al. (2019) .\nMultiple functions implement morphospace plots:\nplot_chronophylomorphospace() implements Sakamoto and Ruta\n(2012) , plot_morphospace()\nimplements Wills et al. (1994) ,\nplot_changes_on_tree() implements Wang and Lloyd (2016)\n, and plot_morphospace_stack()\nimplements Foote (1993) . Other\nfunctions include safe_taxonomic_reduction(), which implements\nWilkinson (1995) ,\nmap_dollo_changes() implements the Dollo stochastic character\nmapping of Tarver et al. (2018) , and\nestimate_ancestral_states() implements the ancestral state\noptions of Lloyd (2018) .\ncalculate_tree_length() and reconstruct_ancestral_states()\nimplements the generalised algorithms from Swofford and\nMaddison (1992; no doi).", "Encoding": "UTF-8", "License": "GPL (>=2)", "LazyData": "yes", "ByteCompile": "yes", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libglpk-dev libgmp3-dev libxml2-dev libx11-dev", "Repository": "https://graemetlloyd.r-universe.dev", "Date/Publication": "2026-02-05 22:44:18 UTC", "RemoteUrl": "https://github.com/graemetlloyd/claddis", "RemoteRef": "HEAD", "RemoteSha": "7f5de57ced981c7c01d164dd97f0bb1f69abb7b5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 07:10:58 UTC", "User": "root" }, "Author": "Graeme T. Lloyd [aut, cre, cph],\nThomas Guillerme [aut, cph],\nJen Hoyal Cuthill [aut, cph],\nEmma Sherratt [aut, cph],\nSteve C. Wang [aut, cph]", "MD5sum": "3e388a7985d45151227f02138db6bae1", "_user": "graemetlloyd", "_type": "src", "_file": "Claddis_0.7.0.tar.gz", "_fileid": "a95c4402a0608e9f75cbfb858834695c5354c259d1380a98ad4b5cee8d8f4358", "_filesize": 2801037, "_sha256": "a95c4402a0608e9f75cbfb858834695c5354c259d1380a98ad4b5cee8d8f4358", "_created": "2026-06-05T07:10:58.000Z", "_published": "2026-06-05T07:15:35.768Z", "_distro": "noble", "_jobs": [ { "job": 79681235622, "time": 164, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7430891340" }, { "job": 79681235606, "time": 177, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7430895044" }, { "job": 79681235603, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7430892814" }, { "job": 79681235618, "time": 155, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7430906075" }, { "job": 79680706090, "time": 250, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430847162" }, { "job": 79681235619, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430879870" }, { "job": 79681235630, "time": 121, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7430880313" }, { "job": 79681235628, "time": 138, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "" }, { "job": 79681235656, "time": 129, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7430882577" } ], "_buildurl": "https://github.com/r-universe/graemetlloyd/actions/runs/27000831727", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/graemetlloyd/claddis", "_commit": { "id": "7f5de57ced981c7c01d164dd97f0bb1f69abb7b5", "author": "Graeme T. Lloyd ", "committer": "Graeme T. Lloyd ", "message": "Fixed some typos.\n", "time": 1770331458 }, "_maintainer": { "name": "Graeme T. Lloyd", "email": "graemetlloyd@gmail.com", "login": "graemetlloyd", "twitter": "@GraemeTLloyd", "description": "", "uuid": 7533214 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "phytools", "role": "Depends" }, { "package": "strap", "role": "Depends" }, { "package": "clipr", "role": "Imports" }, { "package": "geoscale", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "multicool", "role": "Imports" }, { "package": "partitions", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rgl", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "graemetlloyd", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2026-04", "n": 1 }, { "week": "2026-05", "n": 1 }, { "week": "2026-06", "n": 1 } ], "_tags": [], "_stars": 14, "_contributors": [ { "user": "graemetlloyd", "count": 1083, "uuid": 7533214 }, { "user": "dwbapst", "count": 11, "uuid": 1561903 }, { "user": "emsherratt", "count": 3, "uuid": 6485036 }, { "user": "tguillerme", "count": 1, "uuid": 3206086 } ], "_userbio": { "uuid": 7533214, "type": "user", "name": "Graeme T. Lloyd" }, "_downloads": { "count": 483, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Claddis" }, "_mentions": 8, "_devurl": "https://github.com/graemetlloyd/claddis", "_searchresults": 80, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/Claddis.html", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/graemetlloyd/claddis", "_realowner": "graemetlloyd", "_cranurl": true, "_releases": [ { "version": "0.1", "date": "2015-04-28" }, { "version": "0.3.0", "date": "2019-02-12" }, { "version": "0.3.4", "date": "2019-12-05" }, { "version": "0.6.1", "date": "2020-08-26" }, { "version": "0.6.3", "date": "2020-09-26" }, { "version": "0.7.0", "date": "2024-09-03" } ], "_exports": [ "add_polymorphisms_to_costmatrix", "add_uncertainties_to_costmatrix", "align_matrix_block", "assign_taxa_to_bins", "bin_changes", "bin_character_completeness", "bin_edge_lengths", "build_cladistic_matrix", "calculate_g", "calculate_gmax", "calculate_kardashian_index", "calculate_morphological_distances", "calculate_MPD", "calculate_tree_length", "calculate_WMPD", "check_cladisticMatrix", "check_costMatrix", "check_stateGraph", "check_taxonGroups", "check_timeBins", "classify_costmatrix", "compactify_cladistic_matrix", "convert_adjacency_matrix_to_costmatrix", "convert_costmatrix_to_stategraph", "convert_state_tree_to_adjacency_matrix", "convert_stategraph_to_costmatrix", "count_cherries", "date_nodes", "drop_time_tip", "estimate_ancestral_states", "estimate_squared_change_ancestors", "find_costmatrix_minimum_span", "find_descendant_edges", "find_linked_edges", "find_minimum_spanning_edges", "find_mrca", "find_shortest_costmatrix_path", "find_stategraph_minimum_span", "find_time_bin_midpoints", "find_unique_trees", "fix_costmatrix", "fix_root_time", "is_graph_connected", "is.cladisticMatrix", "is.costMatrix", "is.stateGraph", "is.taxonGroups", "is.timeBins", "locate_bracket_positions", "make_costmatrix", "make_labels", "map_dollo_changes", "match_tree_edges", "ordinate_cladistic_matrix", "partition_time_bins", "permute_all_polymorphisms", "permute_all_treeshape_labellings", "permute_all_uncertainties", "permute_combinations_with_replacement", "permute_connected_graphs", "permute_costmatrices", "permute_graph_splits", "permute_restricted_compositions", "permute_tipstates", "permute_treeshapes", "plot_changes_on_tree", "plot_chronophylomorphospace", "plot_morphospace", "plot_morphospace_stack", "plot_multi_morphospace", "plot_rates_character", "plot_rates_time", "plot_rates_tree", "print.cladisticMatrix", "print.costMatrix", "print.stateGraph", "print.taxonGroups", "print.timeBins", "prune_cladistic_matrix", "read_nexus_matrix", "reconstruct_ancestral_states", "safe_taxonomic_reduction", "safe_taxonomic_reinsertion", "split_out_subgraphs", "test_rates", "trim_marginal_whitespace", "trim_matrix", "write_nexus_matrix", "write_tnt_matrix" ], "_datasets": [ { "name": "day_2016", "title": "Character-taxon matrix from Day et al. 2016", "object": "day_2016", "class": [ "cladisticMatrix" ], "fields": [], "table": false, "tojson": false }, { "name": "gauthier_1986", "title": "Character-taxon matrix from Gauthier 1986", "object": "gauthier_1986", "class": [ "cladisticMatrix" ], "fields": [], "table": false, "tojson": false }, { "name": "michaux_1989", "title": "Character-taxon matrix from Michaux 1989", "object": "michaux_1989", "class": [ "cladisticMatrix" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "Claddis-package", "title": "Measuring Morphological Diversity and Evolutionary Tempo Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.", "topics": [ "Claddis-package", "Claddis" ] }, { "page": "add_polymorphisms_to_costmatrix", "title": "Adds polymorphisms to a costmatrix", "topics": [ "add_polymorphisms_to_costmatrix" ] }, { "page": "add_uncertainties_to_costmatrix", "title": "Adds uncertainties to a costmatrix", "topics": [ "add_uncertainties_to_costmatrix" ] }, { "page": "align_matrix_block", "title": "Aligns a phylogenetic matrix block", "topics": [ "align_matrix_block" ] }, { "page": "assign_taxa_to_bins", "title": "Assign taxa to time bins", "topics": [ "assign_taxa_to_bins" ] }, { "page": "bin_changes", "title": "Counts the changes in a series of time bins", "topics": [ "bin_changes" ] }, { "page": "bin_character_completeness", "title": "Phylogenetic character completeness in time-bins", "topics": [ "bin_character_completeness" ] }, { "page": "bin_edge_lengths", "title": "Edge-lengths present in time-bins", "topics": [ "bin_edge_lengths" ] }, { "page": "build_cladistic_matrix", "title": "Creates a morphological data file from a matrix", "topics": [ "build_cladistic_matrix" ] }, { "page": "calculate_g", "title": "Calculate the maximum tree length, g, under parsimony", "topics": [ "calculate_g" ] }, { "page": "calculate_gmax", "title": "Calculate the maximum possible tree length, gmax, under parsimony", "topics": [ "calculate_gmax" ] }, { "page": "calculate_kardashian_index", "title": "Calculates a researcher's Kardashian Index", "topics": [ "calculate_kardashian_index" ] }, { "page": "calculate_morphological_distances", "title": "Get distance matrices from a cladistic matrix", "topics": [ "calculate_morphological_distances" ] }, { "page": "calculate_MPD", "title": "Calculate mean pairwise distances", "topics": [ "calculate_MPD" ] }, { "page": "calculate_tree_length", "title": "Calculates the parsimony length of a set of phylogenetic tree(s)", "topics": [ "calculate_tree_length" ] }, { "page": "calculate_WMPD", "title": "Calculate weighted mean pairwise distances", "topics": [ "calculate_WMPD" ] }, { "page": "check_cladisticMatrix", "title": "Check cladisticMatrix object for errors", "topics": [ "check_cladisticMatrix" ] }, { "page": "check_costMatrix", "title": "Check a costMatrix object for errors", "topics": [ "check_costMatrix" ] }, { "page": "check_stateGraph", "title": "Check a stateGraph object for errors", "topics": [ "check_stateGraph" ] }, { "page": "check_taxonGroups", "title": "Check taxonGroups object for errors", "topics": [ "check_taxonGroups" ] }, { "page": "check_timeBins", "title": "Check timeBins object for errors", "topics": [ "check_timeBins" ] }, { "page": "classify_costmatrix", "title": "Classify a costmatrix character", "topics": [ "classify_costmatrix" ] }, { "page": "compactify_cladistic_matrix", "title": "Collapses matrix to unique character state distributions", "topics": [ "compactify_cladistic_matrix" ] }, { "page": "convert_adjacency_matrix_to_costmatrix", "title": "Converts an adjacency matrix to a costmatrix", "topics": [ "convert_adjacency_matrix_to_costmatrix" ] }, { "page": "convert_costmatrix_to_stategraph", "title": "Convert a costmatrix to a minimal state graph", "topics": [ "convert_costmatrix_to_stategraph" ] }, { "page": "convert_state_tree_to_adjacency_matrix", "title": "Converts a character state tree to an adjacency matrix", "topics": [ "convert_state_tree_to_adjacency_matrix" ] }, { "page": "convert_stategraph_to_costmatrix", "title": "Convert a minimal state graph to a costmatrix", "topics": [ "convert_stategraph_to_costmatrix" ] }, { "page": "count_cherries", "title": "Counts the number of cherries in a tree", "topics": [ "count_cherries" ] }, { "page": "date_nodes", "title": "Returns node ages for a time-scaled tree", "topics": [ "date_nodes" ] }, { "page": "day_2016", "title": "Character-taxon matrix from Day et al. 2016", "topics": [ "day_2016" ] }, { "page": "drop_time_tip", "title": "Drop tips from a time-scaled tree", "topics": [ "drop_time_tip" ] }, { "page": "estimate_ancestral_states", "title": "Ancestral Character State Estimation", "topics": [ "estimate_ancestral_states" ] }, { "page": "estimate_squared_change_ancestors", "title": "Estimate ancestral states for a continuous character under squared-change parsimony", "topics": [ "estimate_squared_change_ancestors" ] }, { "page": "find_costmatrix_minimum_span", "title": "Finds a minimum spanning tree of a costmatrix", "topics": [ "find_costmatrix_minimum_span" ] }, { "page": "find_descendant_edges", "title": "Gets descendant edges of an internal node", "topics": [ "find_descendant_edges" ] }, { "page": "find_linked_edges", "title": "Find linked edges for a tree", "topics": [ "find_linked_edges" ] }, { "page": "find_minimum_spanning_edges", "title": "Get edges of minimum spanning tree", "topics": [ "find_minimum_spanning_edges" ] }, { "page": "find_mrca", "title": "Find ancestor", "topics": [ "find_mrca" ] }, { "page": "find_shortest_costmatrix_path", "title": "Finds the shortest path between two states in a costmatrix", "topics": [ "find_shortest_costmatrix_path" ] }, { "page": "find_stategraph_minimum_span", "title": "Finds a minimum spanning tree of a stategraph", "topics": [ "find_stategraph_minimum_span" ] }, { "page": "find_time_bin_midpoints", "title": "Find time bin midpoints", "topics": [ "find_time_bin_midpoints" ] }, { "page": "find_unique_trees", "title": "Finds only the unique topologies amongst a set", "topics": [ "find_unique_trees" ] }, { "page": "fix_costmatrix", "title": "Fixes a costmatrix that has inconsistent costs", "topics": [ "fix_costmatrix" ] }, { "page": "fix_root_time", "title": "Fixes root.time after taxa have been pruned from a tree", "topics": [ "fix_root_time" ] }, { "page": "gauthier_1986", "title": "Character-taxon matrix from Gauthier 1986", "topics": [ "gauthier_1986" ] }, { "page": "is_graph_connected", "title": "Is a graph connected?", "topics": [ "is_graph_connected" ] }, { "page": "is.cladisticMatrix", "title": "Cladistic matrix class", "topics": [ "is.cladisticMatrix" ] }, { "page": "is.costMatrix", "title": "Costmatrix class", "topics": [ "is.costMatrix" ] }, { "page": "is.stateGraph", "title": "Stategraph class", "topics": [ "is.stateGraph" ] }, { "page": "is.taxonGroups", "title": "Taxon groups class", "topics": [ "is.taxonGroups" ] }, { "page": "is.timeBins", "title": "Time bins class", "topics": [ "is.timeBins" ] }, { "page": "locate_bracket_positions", "title": "Locates matching positions for sets of brackets in a text string", "topics": [ "locate_bracket_positions" ] }, { "page": "make_costmatrix", "title": "Make a costmatrix for a given set of states", "topics": [ "make_costmatrix" ] }, { "page": "make_labels", "title": "Make unique text labels", "topics": [ "make_labels" ] }, { "page": "map_dollo_changes", "title": "Stochastic Character Map For Dollo Character", "topics": [ "map_dollo_changes" ] }, { "page": "match_tree_edges", "title": "Edge matching function", "topics": [ "match_tree_edges" ] }, { "page": "michaux_1989", "title": "Character-taxon matrix from Michaux 1989", "topics": [ "michaux_1989" ] }, { "page": "ordinate_cladistic_matrix", "title": "Principal Coordinates on a Cladistic Matrix", "topics": [ "ordinate_cladistic_matrix" ] }, { "page": "partition_time_bins", "title": "Time bin partitioner", "topics": [ "partition_time_bins" ] }, { "page": "permute_all_polymorphisms", "title": "Permute all possible polymorphisms for a given set of states", "topics": [ "permute_all_polymorphisms" ] }, { "page": "permute_all_treeshape_labellings", "title": "Label treeshapes", "topics": [ "permute_all_treeshape_labellings" ] }, { "page": "permute_all_uncertainties", "title": "Permute all possible uncertainties for a given set of states", "topics": [ "permute_all_uncertainties" ] }, { "page": "permute_combinations_with_replacement", "title": "Permute all combinations of x of size m with replacement", "topics": [ "permute_combinations_with_replacement" ] }, { "page": "permute_connected_graphs", "title": "Permute all connected graphs", "topics": [ "permute_connected_graphs" ] }, { "page": "permute_costmatrices", "title": "Permute costmatrices", "topics": [ "permute_costmatrices" ] }, { "page": "permute_graph_splits", "title": "Permute all ways to split a graph", "topics": [ "permute_graph_splits" ] }, { "page": "permute_restricted_compositions", "title": "Permute all ways to place n items into m bins", "topics": [ "permute_restricted_compositions" ] }, { "page": "permute_tipstates", "title": "Permute all tip states on a tree", "topics": [ "permute_tipstates" ] }, { "page": "permute_treeshapes", "title": "Permute all treeshapes of N tips", "topics": [ "permute_treeshapes" ] }, { "page": "plot_changes_on_tree", "title": "Plots character changes on branches", "topics": [ "plot_changes_on_tree" ] }, { "page": "plot_chronophylomorphospace", "title": "Chronophylomorphospace Plot", "topics": [ "plot_chronophylomorphospace" ] }, { "page": "plot_morphospace", "title": "Plot Morphopace", "topics": [ "plot_morphospace" ] }, { "page": "plot_morphospace_stack", "title": "Plot stacked ordination spaces", "topics": [ "plot_morphospace_stack" ] }, { "page": "plot_multi_morphospace", "title": "Plot Multiple Morphopaces", "topics": [ "plot_multi_morphospace" ] }, { "page": "plot_rates_character", "title": "Visualize a rate test time series", "topics": [ "plot_rates_character" ] }, { "page": "plot_rates_time", "title": "Visualize a rate test time series", "topics": [ "plot_rates_time" ] }, { "page": "plot_rates_tree", "title": "Visualize a rate test time series", "topics": [ "plot_rates_tree" ] }, { "page": "print.cladisticMatrix", "title": "Compact display of a cladistic matrix", "topics": [ "print.cladisticMatrix" ] }, { "page": "print.costMatrix", "title": "Compact display of a costmatrix", "topics": [ "print.costMatrix" ] }, { "page": "print.stateGraph", "title": "Compact display of a stategraph", "topics": [ "print.stateGraph" ] }, { "page": "print.taxonGroups", "title": "Compact display of taxon groups", "topics": [ "print.taxonGroups" ] }, { "page": "print.timeBins", "title": "Compact display of time bins", "topics": [ "print.timeBins" ] }, { "page": "prune_cladistic_matrix", "title": "Prunes a character matrix of characters or taxa", "topics": [ "prune_cladistic_matrix" ] }, { "page": "read_nexus_matrix", "title": "Reads in a morphological #NEXUS data file", "topics": [ "read_nexus_matrix" ] }, { "page": "reconstruct_ancestral_states", "title": "Determine maximum parsimony ancestral state reconstruction(s)", "topics": [ "reconstruct_ancestral_states" ] }, { "page": "safe_taxonomic_reduction", "title": "Safe Taxonomic Reduction", "topics": [ "safe_taxonomic_reduction" ] }, { "page": "safe_taxonomic_reinsertion", "title": "Reinsert Safely Removed Taxa Into A Tree", "topics": [ "safe_taxonomic_reinsertion" ] }, { "page": "split_out_subgraphs", "title": "Split adjacency matrix into subgraphs", "topics": [ "split_out_subgraphs" ] }, { "page": "test_rates", "title": "Discrete character rates across trees, time, and character types", "topics": [ "test_rates" ] }, { "page": 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