Claddis (version 0.7.0)

Claddis-package: Measuring Morphological Diversity and Evolutionary Tempo Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.

Description

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

Author

Graeme T. Lloyd <[e-mail]>

References

Lloyd, G. T., 2016. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biological Journal of the Linnean Society, 118, 131-151.

Examples

# Get morphological distances for Michaux (1989) data set:
distances <- calculate_morphological_distances(cladistic_matrix = michaux_1989)

# Show distances:
distances