strap-package: Stratigraphic Tree Analysis for Palaeontology

Description Details Author(s) References Examples

Description

A series of functions for stratigraphic analysis of phylogenetic trees.

Details

Package: strap
Type: Package
Version: 1.4
Date: 2014-10-31
License: GPL (>=2)
LazyLoad: yes

Author(s)

Mark A. Bell <mark.bell521@gmail.com> and Graeme T. Lloyd <graemetlloyd@gmail.com>

References

Wills, M. A., 1999, Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio. Systematic Biology, 48(3), 559-580.

Examples

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# Calculate stratigraphic fit measures treating ages as ranges:
fit.to.strat.1 <- StratPhyloCongruence(trees=Dipnoi$tree, ages=Dipnoi$ages, rlen=0,
	method="basic", samp.perm=5, rand.perm=5, hard=TRUE,
	randomly.sample.ages=FALSE, fix.topology=FALSE, fix.outgroup=TRUE)
	
fit.to.strat.1$input.tree.results # Show just the output for the input tree(s)

Example output

Loading required package: ape
Loading required package: geoscale

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Fit to stratigraphy measures for 1 input trees have been calculated.            SCI       RCI       GER      MSM*  est.p.SCI     est.p.RCI
tree_1 0.547619 -79.87227 0.7807366 0.2012994 0.01646166 7.024728e-280
           est.p.GER est.p.MSM* GER* GERt    MIG p.Wills
tree_1 5.034901e-251          0    1    1 1754.6       0

strap documentation built on May 2, 2019, 2:26 p.m.