genDensityTree {poweRbal} | R Documentation |
genDensityTree
- Generates a rooted binary tree in phylo
format with the given number of n
leaves under the
density-dependent model.
In the density-dependent tree generation process all species have the same
speciation BIRTHRATE
, but the extinction rates depend on the
number of species (it increases linearly with the number of co-existing
lineages until an equilibrium number is reached at which speciation and
extinction rates are equal).
Extinct species are removed from the tree, i.e., the generated tree contains
only species living at the present.
genDensityTree(n, BIRTHRATE = 1, EQUILIB, TRIES = 5, TIMEperTRY = 0.01)
n |
Integer value that specifies the desired number of leaves, i.e.,
vertices with in-degree 1 and out-degree 0. |
BIRTHRATE |
Positive numeric value (default = 1) which specifies the rate at which the speciation events occur. |
EQUILIB |
Integer value that specifies the equilibrium number. |
TRIES |
Integer value (default = 5) that specifies
the number of attempts to generate a tree with |
TIMEperTRY |
Numeric value (default = 0.01) that specifies the maximum amount of time (in seconds) invested per try. |
genDensityTree
A single tree of class phylo
is
returned.
P. H. Harvey, R. M. May, and S. Nee. Phylogenies without fossils. Evolution, 48(3):523–529, 1994.
genDensityTree(n = 5, EQUILIB = 6)