Claddis

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) ) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) ). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) , Brusatte et al. (2014) , Close et al. (2015) , and Lloyd (2016) , and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) , Wills (1998) , Lloyd (2016) , and Hopkins and St John (2018) . This also includes the GED correction from Lehmann et al. (2019) . Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) , plot_morphospace() implements Wills et al. (1994) , plot_changes_on_tree() implements Wang and Lloyd (2016) , and plot_morphospace_stack() implements Foote (1993) . Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) , map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) , and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) . calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

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