Claddis-package

Claddis

<p>Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.</p>

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 ReadMorphNexus(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are DiscreteCharacterRate(), which implements 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 MorphDistMatrix(), 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>. Multiple functions
implement various morphospace plots: ChronoPhyloMorphospacePlot() implements
Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>,
MorphospacePlot() implements Wills et al. (1994)
<doi:10.1017/S009483730001263X>, PlotCharacterChanges() implements Wang and
Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and StackPlot() implements Foote
(1993) <doi:10.1017/S0094837300015864>. Other functions include
SafeTaxonomicReduction(), which implements Wilkinson (1995)
<doi:10.1093/sysbio/44.4.501>, and DolloSCM() implements the Dollo
stochastic character mapping of Tarver et al. (2018)
<doi:10.1093/gbe/evy096>.

Claddis-package: Measuring Morphological Diversity and Evolutionary Tempo

Description

Arguments

References

Examples