Data from: strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for
the freely available statistical programming language R designed to
perform three main tasks: (1) to time-scale phylogenies of fossil taxa;
(2) to plot those time-scaled trees against stratigraphy; and (3) to
assess congruence between phylogenies and stratigraphy. Time-scaling is
performed with the DatePhylo function, with three approaches offered.
Plotting trees against a choice of five different geological time scaless
is possible using the geoscalePhylo function. Finally, the function
StratPhyloCongruence calculates stratigraphic congruence measures for one
or more input phylogenies, with no taxon limit. All three major congruence
measures are offered: Stratigraphic Consistency Index (SCI), Manhattan
Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt
and GER*), as well as the pseudocongruence measure, the Relative
Completeness Index (RCI). Each measure has an accompanying significance
test that works by comparing the input trees against a user-defined number
of randomly generated topologies with the same taxon set and age ranges.
Additional options for generating these random topologies allow the user
to fix the outgroup or retain the input tree shape to make fairer
comparisons. A tutorial that assumes no prior knowledge of R showcases all
three functions using two different example data sets.