Title: Measuring Morphological Diversity and Evolutionary Tempo
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Description: Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees.

person(given = "Graeme T.", family = "Lloyd",
email = "graemetlloyd@gmail.com", role = c("aut", "cre", "cph")),
person(given = "Thomas", family = "Guillerme", role = c("aut", "cph")),
person(given = "Emma", family = "Sherratt", role = c("aut", "cph")),
person(given = "Steve C.", family = "Wang", role = c("aut", "cph"))
Imports: gdata, graphics, grDevices, stats, utils
Description: 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
functions are DiscreteCharacterRate(), which implements likelihood ratio
tests for discrete character rates introduced across Lloyd et al. (2012)
and MorphDistMatrix(), which implements multiple discrete character
distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998)
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
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)
Author: Graeme T. Lloyd [aut, cre, cph],

Imports: clipr, gdata, graphics, grDevices, stats, utils

Depends: ape, phytools, strap, R (>= 3.5.0)
Imports: clipr, gdata, geoscale, graphics, grDevices, methods, stats,
format with read_nexus_matrix(), and writes to both #NEXUS and TNT format
functions are test_rates(), which implements AIC and likelihood
ratio tests for discrete character rates introduced across Lloyd et al.
and MatrixDistances(), which implements multiple discrete character
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
implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and
safe_taxonomic_reduction(), which implements Wilkinson (1995)
the Dollo stochastic character mapping of Tarver et al. (2018)
the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.