Package: Claddis Type: Package Title: Measuring Morphological Diversity and Evolutionary Tempo Version: 0.6.3 Date: 2020-09-14 Authors@R: c( person(given = "Graeme T.", family = "Lloyd", email = "graemetlloyd@gmail.com", role = c("aut", "cre", "cph")), person(given = "Thomas", family = "Guillerme", role = c("aut", "cph")), person(given = "Emma", family = "Sherratt", role = c("aut", "cph")), person(given = "Steve C.", family = "Wang", role = c("aut", "cph")) ) Maintainer: Graeme T. Lloyd Depends: ape, phytools, strap, R (>= 3.5.0) Imports: clipr, geoscale, graphics, grDevices, methods, stats, utils Suggests: rgl, testthat Description: 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 MatrixDistances(), 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) . Encoding: UTF-8 License: GPL (>= 2) LazyData: yes ByteCompile: yes RoxygenNote: 7.1.0 NeedsCompilation: no Packaged: 2020-09-25 16:04:37 UTC; eargtl Author: Graeme T. Lloyd [aut, cre, cph], Thomas Guillerme [aut, cph], Emma Sherratt [aut, cph], Steve C. Wang [aut, cph] Repository: CRAN Date/Publication: 2020-09-26 04:30:23 UTC