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) ) 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) .

Claddis is an R package designed to import cladistic-type data sets (#NEXUS format) into R and perform disparity and rate tests.

You can install Claddis in R using:


And load it into memory using:


Basic help can be found with:


And clicking on the Index link at the base of the help file will reveal links to every available function.

Note that I have previously produced tutorials for the package here, but that current substantial reworking of the core code means these will no longer function and so the example code in each function's help file is the current best substitute for this.

Claddis is not currently available on CRAN, but version (0.3) can be installed directly from github using the code above. The first formal paper describing Claddis is now published (Lloyd 2016), with further discussion in Lloyd (2018):

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.

Lloyd, G. T., 2018. Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity. Palaeontology, 61, 637-645.


Reference manual

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0.6.3 by Graeme T. Lloyd, a year ago

Browse source code at

Authors: Graeme T. Lloyd [aut, cre, cph] , Thomas Guillerme [aut, cph] , Emma Sherratt [aut, cph] , Steve C. Wang [aut, cph]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports clipr, geoscale, graphics, grDevices, methods, stats, utils

Depends on ape, phytools, strap

Suggests rgl, testthat

Imported by dispRity.

See at CRAN