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 ReadMorphNexus(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are DiscreteCharacterRate(), which implements 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 MorphDistMatrix(), 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>. Multiple functions implement various morphospace plots: ChronoPhyloMorphospacePlot() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, MorphospacePlot() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, PlotCharacterChanges() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and StackPlot() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include SafeTaxonomicReduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, and DolloSCM() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>.

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