Package: Claddis
Type: Package
Title: Measuring Morphological Diversity and Evolutionary Tempo
Version: 0.3.0
Date: 2019-02-12
Authors@R: c(
    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"))
    )
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Depends: ape, phytools, strap
Imports: gdata, graphics, grDevices, stats, utils
Suggests: rgl
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 
    (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>.
Encoding: UTF-8
License: GPL (>= 2)
LazyData: yes
ByteCompile: yes
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-12 12:17:26 UTC; eargtl
Author: Graeme T. Lloyd [aut, cre, cph],
  Thomas Guillerme [aut, cph],
  Emma Sherratt [aut, cph],
  Steve C. Wang [aut, cph]
Repository: CRAN
Date/Publication: 2019-02-12 13:19:36 UTC
