permute_all_uncertainties

Given a set of discrete states, will permute all possible uncertainity combinations of those states.

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).

Graeme T. Lloyd

Claddis

Measuring Morphological Diversity and Evolutionary Tempo

Thomas Guillerme

Jen Hoyal Cuthill

Emma Sherratt

Steve C. Wang

permute_all_uncertainties function

<dl><dt>single_states</dt>
<dd>A vector of single states (e.g., 0, 1, 2 etc.).</dd></dl>

Arguments

Graeme T. Lloyd <a href="/link/graemetlloyd%40gmail.com?package=Claddis&version=0.7.0" data-mini-rdoc="Claddis::graemetlloyd@gmail.com">graemetlloyd@gmail.com</a>

Author

Permute all possible uncertainties for a given set of states — permute_all_uncertainties

<dl>

<dt>single_states</dt>
<dd>A vector of single states (e.g., 0, 1, 2 etc.).</dd>

</dl>

Graeme T. Lloyd <a href='mailto:graemetlloyd@gmail.com'>graemetlloyd@gmail.com</a>

permute_all_uncertainties: Permute all possible uncertainties for a given set of states

Description

Usage

Value

Arguments

Author

Details

See Also

Examples