Claddis: 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) <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).

Version:	0.7.0
Depends:	ape, phytools, strap, R (≥ 3.5.0)
Imports:	clipr, geoscale, graphics, grDevices, methods, multicool, partitions, stats, utils
Suggests:	rgl, testthat
Published:	2024-09-03
DOI:	10.32614/CRAN.package.Claddis
Author:	Graeme T. Lloyd [aut, cre, cph], Thomas Guillerme [aut, cph], Jen Hoyal Cuthill [aut, cph], Emma Sherratt [aut, cph], Steve C. Wang [aut, cph]
Maintainer:	Graeme T. Lloyd <graemetlloyd at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
Citation:	Claddis citation info
Materials:	README, ChangeLog
In views:	Phylogenetics
CRAN checks:	Claddis results

Documentation:

Reference manual:

Claddis.html , Claddis.pdf

Downloads:

Package source:	Claddis_0.7.0.tar.gz
Windows binaries:	r-devel: Claddis_0.7.0.zip, r-release: Claddis_0.7.0.zip, r-oldrel: Claddis_0.7.0.zip
macOS binaries:	r-release (arm64): Claddis_0.7.0.tgz, r-oldrel (arm64): Claddis_0.7.0.tgz, r-release (x86_64): Claddis_0.7.0.tgz, r-oldrel (x86_64): Claddis_0.7.0.tgz
Old sources:	Claddis archive

Reverse dependencies:

Reverse imports:

dispRity

Linking:

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