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: ape, phytools, strap, R (>= 3.5.0)
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: 7.3.1
NeedsCompilation: no
Packaged: 2024-09-03 15:03:47 UTC; eargtl
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]
Repository: CRAN
Date/Publication: 2024-09-03 16:10:05 UTC
Built: R 4.5.0; ; 2025-01-21 17:36:27 UTC; unix
