{
  "_id": "6a49fb729a7b00bcc12f586d",
  "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 <graemetlloyd@gmail.com>",
  "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<doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(),\nand writes to both #NEXUS and TNT format (Goloboff et al.\n(2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions\nare test_rates(), which implements AIC and likelihood ratio\ntests for discrete character rates introduced across Lloyd et\nal. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et\nal. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)\n<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016)\n<doi:10.1111/bij.12746>, and\ncalculate_morphological_distances(), which implements multiple\ndiscrete character distance metrics from Gower (1971)\n<doi:10.2307/2528823>, Wills (1998)\n<doi:10.1006/bijl.1998.0255>, Lloyd (2016)\n<doi:10.1111/bij.12746>, and Hopkins and St John (2018)\n<doi:10.1098/rspb.2018.1784>. This also includes the GED\ncorrection from Lehmann et al. (2019) <doi:10.1111/pala.12430>.\nMultiple functions implement morphospace plots:\nplot_chronophylomorphospace() implements Sakamoto and Ruta\n(2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace()\nimplements Wills et al. (1994) <doi:10.1017/S009483730001263X>,\nplot_changes_on_tree() implements Wang and Lloyd (2016)\n<doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack()\nimplements Foote (1993) <doi:10.1017/S0094837300015864>. Other\nfunctions include safe_taxonomic_reduction(), which implements\nWilkinson (1995) <doi:10.1093/sysbio/44.4.501>,\nmap_dollo_changes() implements the Dollo stochastic character\nmapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and\nestimate_ancestral_states() implements the ancestral state\noptions of Lloyd (2018) <doi:10.1111/pala.12380>.\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",
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  "Repository": "https://graemetlloyd.r-universe.dev",
  "Date/Publication": "2026-02-05 22:44:18 UTC",
  "RemoteUrl": "https://github.com/graemetlloyd/claddis",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-05 06:32:28 UTC",
    "User": "root"
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  "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]",
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  "_expires": "2026-10-13T06:36:32.000Z",
  "_created": "2026-07-05T06:32:28.000Z",
  "_published": "2026-07-05T06:36:34.382Z",
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  "_buildurl": "https://github.com/r-universe/graemetlloyd/actions/runs/28732019279",
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  "_upstream": "https://github.com/graemetlloyd/claddis",
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    "author": "Graeme T. Lloyd <graemetlloyd@gmail.com>",
    "committer": "Graeme T. Lloyd <graemetlloyd@gmail.com>",
    "message": "Fixed some typos.\n",
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  "_assets": [
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    "extra/contents.json",
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    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/graemetlloyd/claddis",
  "_realowner": "graemetlloyd",
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  "_releases": [
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      "date": "2015-04-28"
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    {
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  ],
  "_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"
      ]
    },
    {
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