strap-package: Measuring Morphological Diversity and Evolutionary Tempo
In strap: Stratigraphic Tree Analysis for Palaeontology

strap-package

R Documentation

Measuring Morphological Diversity and Evolutionary Tempo

Description

A series of functions for stratigraphic analysis of phylogenetic trees.

Author(s)

Graeme T. Lloyd <graemetlloyd@gmail.com>>

References

Bell, M. A. and Lloyd, G. T., 2015. strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology, 58, 379-389.

Examples


# 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,
  outgroup.taxon = "Psarolepis_romeri")

# Show just the output for the input tree(s)
fit.to.strat.1$input.tree.results

strap documentation built on June 13, 2022, 9:05 a.m.