Claddis

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).

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