paleotree.record.to.fossils: Transforms a fossilRecordSimulation object from package...

In fossilsim/fossilsim: Simulation of Fossil and Taxonomy Data

Transforms a fossilRecordSimulation object from package paleotree to a tree and taxonomy and fossils objects.

Description

The returned tree is in paleotree format, with zero-length edges leading to tips at bifurcation and anagenetic events. Fossils and taxonomy are only specified on non-zero-length edges. The label assigned to the parent of the origin or root will be zero.

Usage

paleotree.record.to.fossils(record, alphanumeric = TRUE)

Arguments

record	fossilRecordSimulation object.
alphanumeric	If TRUE function will return alphanumeric species labels (i.e. species labels contain the "t" prefix) (default). If FALSE function will return numeric only species labels.

Value

A list containing the converted tree, taxonomy and fossils

See Also

taxonomy, fossils, fossils.to.paleotree.record

Examples

if (requireNamespace("paleotree", quietly = TRUE)) {
# simulate record
record = paleotree::simFossilRecord(p=0.1, q=0.1,r=0.1, nruns=1, nTotalTaxa=c(30,40),
    nExtant=0, nSamp = c(5,25))

# transform format
l_tf = paleotree.record.to.fossils(record)
l_tf$tree
l_tf$taxonomy
l_tf$fossils
}

fossilsim/fossilsim documentation built on April 18, 2024, 10:29 a.m.