strap-package | R Documentation |
A series of functions for stratigraphic analysis of phylogenetic trees.
Graeme T. Lloyd <graemetlloyd@gmail.com>>
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.
# 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
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