estimate_node_heights: Calculate expected time to branching point of a species tree
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Details Value References Examples

Calculates the expected time to branching point of a species tree for a birth-death simulation given a speciation and extinction rate and a number of leaves, and a branching point.

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estimate_node_heights(lambda, mu, n, k = 1)

node_heights(lambda, mu, n, k = 1)

`lambda`	speciation rate
`mu`	extinction rate
`n`	number of tips on tree
`k`	branching point (k = 1 is the root and is the default)

By default this branching point is 1 which corresponds to the root, k = 2 corresponds to the first branching point after the root, k = 3 the second, and so on. For more details see Gernhard 2008.

The expected branching time

Gernhard, T. (2008). The conditioned reconstructed process. Journal of theoretical biology, 253(4), 769-778.

spec_rate <- 1.0
ext_rate <- 0.5
nt <- 10
node_heights(lambda = spec_rate, mu = ext_rate, n = nt)

node_heights(lambda = spec_rate, mu = ext_rate, n = nt, k = 2)