A series of functions for stratigraphic analysis of phylogenetic trees.
Graeme T. Lloyd <firstname.lastname@example.org>>
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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