genBiSSETree {poweRbal} | R Documentation |
Generation of rooted binary trees under the BiSSE model
Description
genBiSSETree
- Generates a rooted binary tree in phylo
format with the given number of n
leaves under the BiSSE model.
In the BiSSE model all species have a state, either A or B, and depending on
the state a speciation rate BIRTHRATES
, an extinction rate
DEATHRATES
as well as a transition rate to the other state
TRANSRATES
.
Extinct species are removed from the tree, i.e., the generated tree contains
only species living at the present.
Usage
genBiSSETree(
n,
BIRTHRATES = c(1, 1),
DEATHRATES = c(0, 0),
TRANSRATES,
TRIES = 5,
TIMEperTRY = 0.1
)
Arguments
n |
Integer value that specifies the desired number of leaves, i.e.,
vertices with in-degree 1 and out-degree 0. |
BIRTHRATES |
Numeric vector (default = c(1,1)) which specifies the speciation rates in state A and B (vector with 2 values >=0, one value >0). |
DEATHRATES |
Numeric vector (default = c(0,0)) which specifies the extinction rates in state A and B (vector with 2 values >=0). |
TRANSRATES |
Numeric vector which specifies the transition rates from A to B and from B to A (vector with 2 values >0). |
TRIES |
Integer value (default = 5) that specifies
the number of attempts to generate a tree with |
TIMEperTRY |
Numeric value (default = 0.1) that specifies the maximum amount of time (in seconds) invested per try. |
Value
genBiSSETree
A single tree of class phylo
is
returned.
References
This function uses the
tree.bisse
function of thediversitree
package (R. G. FitzJohn. Diversitree: Comparative Phylogenetic Analyses of Diversification in R. Methods in Ecology and Evolution, 3(6):1084-1092, 2012).
W. P. Maddison, P. E. Midford, and S. P. Otto. Estimating a binary character’s effect on speciation and extinction. Systematic Biology, 56(5):701–710, 2007.
Examples
if (requireNamespace("diversitree", quietly = TRUE)) {
genBiSSETree(n = 5, BIRTHRATES = c(1,2), DEATHRATES = c(0,0),
TRANSRATES = c(0.1,0.3))
}