SafeTaxonomicReinsertion

A Newick-formatted tree file containing tree(s) without safely removed taxa.

treefile.in

A file name where the newly generated trees will be written out to (required).

treefile.out

The safe taxonomic reduction table as generated by <a rd-options="" href="/link/SafeTaxonomicReduction?package=Claddis&version=0.3.4" data-mini-rdoc="Claddis::SafeTaxonomicReduction">SafeTaxonomicReduction</a>.

str.list

An optional for what to do with taxa that have more than one possible reinsertion position. Options are <code>"exclude"</code> (does not reinsert them; the default) or <code>"random"</code> (picks one of the possible positions and uses that; will vary stochastically if multiple trees exist).

multi.placements

Following Safe Taxonomic Reduction reinsert removed taxa.

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>.

Graeme T. Lloyd

Claddis

Measuring Morphological Diversity and Evolutionary Tempo

Thomas Guillerme

Emma Sherratt

Steve C. Wang

SafeTaxonomicReinsertion function

The safe taxonomic reduction table as generated by <a rd-options='' href='SafeTaxonomicReduction'>SafeTaxonomicReduction</a>.

SafeTaxonomicReinsertion: Reinsert Safely Removed Taxa Into A Tree

Description

Usage

Arguments

Value

Details

Examples