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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 |
| Reference manual: | Claddis.pdf |
| 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 imports: | dispRity |
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