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:
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