fossils.to.pyrate | R Documentation |
Generate output in the format used by the program PyRate
fossils.to.pyrate( fossils, python = TRUE, traits = NULL, cutoff = NULL, random = FALSE, min = NULL, exclude.extant.singletons = TRUE, file = "", use.sp.names = FALSE )
fossils |
Fossils object. |
python |
If TRUE the function outputs the data in the python format used by PyRate (default). If FALSE the function outputs a tab-delimited table used by tools associated with PyRate. |
traits |
Vector of trait values equal to the number of unique species in the fossils dataframe.
The order should correspond to the order in which they appear in |
cutoff |
Exclude occurrences with age uncertainty greater than this value i.e. |
random |
If TRUE use a random number from within the interval U(hmin, hmax) for specimen ages,
otherwise use the midpoint of this interval (default). Applicable only when |
min |
Value used to represent the minimum possible interval age of extinct specimens with |
exclude.extant.singletons |
If TRUE exclude species that have extant samples only (default = TRUE). |
file |
Output file name. |
use.sp.names |
If TRUE use the value in fossils$sp as the complete taxon name, otherwise the function adds the prefix "taxa" (default = FALSE). |
set.seed(123) # simulate tree t = ape::rtree(6) # assign a max age based on tree height max.age = tree.max(t) # define a set of non-uniform length intervals times = c(0, sort(runif(3, min = 0, max = max.age)), max.age) rates = c(1,2,3,4) # simulate fossils reflect age uncertainty f = sim.fossils.intervals(tree = t, interval.ages = times, rates = rates, use.exact.times = FALSE) # simulate extant samples rho = 1 f = sim.extant.samples(f, t, rho = 1) plot(f, t) # generate input files for pyrate fossils.to.pyrate(f) fossils.to.pyrate(f, python = FALSE) # add trait values traits = runif(length(unique(f$sp))) fossils.to.pyrate(f, traits = traits)
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