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).
- A General Coefficient of Similarity and Some of Its Properties
- A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies
- Biases with the Generalized Euclidean Distance measure in disparity analyses with high levels of missing data
- Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity
- Discordance and concordance between morphological and taxonomic diversity
- Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods
- Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions
- Evidence for a Mid-Jurassic Adaptive Radiation in Mammals
- Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition
- IDENTIFYING HETEROGENEITY IN RATES OF MORPHOLOGICAL EVOLUTION: DISCRETE CHARACTER CHANGE IN THE EVOLUTION OF LUNGFISH (SARCOPTERYGII; DIPNOI)
- Journeys through discrete‐character morphospace: synthesizing phylogeny, tempo, and disparity
- Nexus: An Extensible File Format for Systematic Information
- Rates of morphological evolution are heterogeneous in Early Cretaceous birds
- TNT, a free program for phylogenetic analysis
- Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss
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