Package: Claddis 0.7.0

Graeme T. Lloyd

Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

Authors:Graeme T. Lloyd [aut, cre, cph], Thomas Guillerme [aut, cph], Jen Hoyal Cuthill [aut, cph], Emma Sherratt [aut, cph], Steve C. Wang [aut, cph]

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Peer review:

Bug tracker:https://github.com/graemetlloyd/claddis/issues

On CRAN:

88 exports 12 stars 3.30 score 65 dependencies 2 dependents 8 mentions 69 scripts 463 downloads

Last updated 4 days agofrom:66d0d06037. Checks:OK: 7. Indexed: no.

Exports:add_polymorphisms_to_costmatrixadd_uncertainties_to_costmatrixalign_matrix_blockassign_taxa_to_binsbin_changesbin_character_completenessbin_edge_lengthsbuild_cladistic_matrixcalculate_gcalculate_gmaxcalculate_kardashian_indexcalculate_morphological_distancescalculate_MPDcalculate_tree_lengthcalculate_WMPDcheck_cladisticMatrixcheck_costMatrixcheck_stateGraphcheck_taxonGroupscheck_timeBinsclassify_costmatrixcompactify_cladistic_matrixconvert_adjacency_matrix_to_costmatrixconvert_costmatrix_to_stategraphconvert_state_tree_to_adjacency_matrixconvert_stategraph_to_costmatrixcount_cherriesdate_nodesdrop_time_tipestimate_ancestral_statesestimate_squared_change_ancestorsfind_costmatrix_minimum_spanfind_descendant_edgesfind_linked_edgesfind_minimum_spanning_edgesfind_mrcafind_shortest_costmatrix_pathfind_stategraph_minimum_spanfind_time_bin_midpointsfind_unique_treesfix_costmatrixfix_root_timeis_graph_connectedis.cladisticMatrixis.costMatrixis.stateGraphis.taxonGroupsis.timeBinslocate_bracket_positionsmake_costmatrixmake_labelsmap_dollo_changesmatch_tree_edgesordinate_cladistic_matrixpartition_time_binspermute_all_polymorphismspermute_all_treeshape_labellingspermute_all_uncertaintiespermute_connected_graphspermute_costmatricespermute_graph_splitspermute_restricted_compositionspermute_tipstatespermute_treeshapesplot_changes_on_treeplot_chronophylomorphospaceplot_morphospaceplot_morphospace_stackplot_multi_morphospaceplot_rates_characterplot_rates_timeplot_rates_treeprint.cladisticMatrixprint.costMatrixprint.stateGraphprint.taxonGroupsprint.timeBinsprune_cladistic_matrixread_nexus_matrixreconstruct_ancestral_statessafe_taxonomic_reductionsafe_taxonomic_reinsertionsplit_out_subgraphstest_ratestrim_marginal_whitespacetrim_matrixwrite_nexus_matrixwrite_tnt_matrix

Dependencies:apeclicliprclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParallelexpmfansifarverfastmatchforeachgenericsgeoscaleggplot2ggseqlogogluegmpgtableigraphisobanditeratorslabelinglatticelifecyclemagrittrmapsMASSmathjaxrMatrixmgcvmnormtmulticoolmunsellnlmenumDerivoptimParallelpartitionspbapplyphangornphytoolspillarpkgconfigpolynomquadprogR6rbibutilsRColorBrewerRcppRdpackrlangscalesscatterplot3dsetsstraptibbleutf8vctrsviridisLitewithr