Package: Claddis
Type: Package
Title: Measuring Morphological Diversity and Evolutionary Tempo
Version: 0.7.0
Date: 2024-09-01
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 = "Jen", family = "Hoyal Cuthill", 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: R (>= 4.1.0), ape, phytools, strap
Imports: clipr, geoscale, graphics, grDevices, methods, multicool,
        partitions, stats, utils
Suggests: rgl, testthat
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 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).
Encoding: UTF-8
License: GPL (>=2)
LazyData: yes
ByteCompile: yes
RoxygenNote: 7.3.2
Config/pak/sysreqs: libglpk-dev libgmp3-dev libxml2-dev libx11-dev
Repository: https://graemetlloyd.r-universe.dev
Date/Publication: 2026-02-05 22:44:18 UTC
RemoteUrl: https://github.com/graemetlloyd/claddis
RemoteRef: HEAD
RemoteSha: 7f5de57ced981c7c01d164dd97f0bb1f69abb7b5
NeedsCompilation: no
Packaged: 2026-06-05 07:10:58 UTC; root
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]