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).
