Claddis (0.3.0)

Measuring Morphological Diversity and Evolutionary Tempo.

http://cran.r-project.org/web/packages/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 ReadMorphNexus(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) ). Main functions are DiscreteCharacterRate(), which implements 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 MorphDistMatrix(), which implements multiple discrete character distance metrics from Gower (1971) , Wills (1998) , Lloyd (2016) , and Hopkins and St John (2018) . Multiple functions implement various morphospace plots: ChronoPhyloMorphospacePlot() implements Sakamoto and Ruta (2012) , MorphospacePlot() implements Wills et al. (1994) , PlotCharacterChanges() implements Wang and Lloyd (2016) , and StackPlot() implements Foote (1993) . Other functions include SafeTaxonomicReduction(), which implements Wilkinson (1995) , and DolloSCM() implements the Dollo stochastic character mapping of Tarver et al. (2018) .

Maintainer: Graeme T. Lloyd
Author(s): Graeme T. Lloyd [aut, cre, cph], Thomas Guillerme [aut, cph], Emma Sherratt [aut, cph], Steve C. Wang [aut, cph]

License: GPL (>= 2)

Uses: ape, gdata, phytools, strap, rgl

Released 10 months ago.