correlated.trees: Simulate correlated branch lengths among loci on a phylogeny...

In dosreislab/simclock: Simulate trees under relaxed clocks

Simulate correlated branch lengths among loci on a phylogeny under a relaxed clock

Description

Simulate correlated branch lengths among loci on a phylogeny under a relaxed clock

Usage

correlated.trees(tree, model, r, s2, nloci, corr)

Arguments

tree	an object of class phylo representing a bifurcating phylogeny
model	character, the relaxed clock model
r	numeric, the mean rate in substitutions per site
s2	numeric, the rate "diffusion" parameter for the relaxed clocks
nloci	numeric, the number of trees to simulate (one per locus)
corr	numeric, the correlation of log rates among loci

Details

A total of nloci trees are simulated, with the log-rates for branches across trees having correlation corr.

Value

A list with two elements: A list of length nloci of trees of class phylo with branch lengths in substitutions per site, and a matrix of branch rates for each locus.

Author(s)

Mario dos Reis

See Also

relaxed.tree to simulate a single tree.

Examples

require(ape)
par(mfrow=c(2,3))

data(pri10s)
# ILN model:
# Simulate using autocorrelated log-normal rates on a primate phylogeny,
# with no correlation among three loci:
iln0 <- correlated.trees(pri10s, model="iln", r=.04e-2, s2=.1, 3, 0)
lapply(iln0$trees, plot)
# Repeat with strong correlation among loci:
ilnc <- correlated.trees(pri10s, model="iln", r=.04e-2, s2=.1, 3, 0.9)
lapply(ilnc$trees, plot)

# GBM model:
# Simulate using autocorrelated log-normal rates on a primate phylogeny,
# with no correlation among three loci:
gbm0 <- correlated.trees(pri10s, model="gbm", r=.04e-2, s2=.26e-2, 3, 0)
lapply(gbm0$trees, plot)
# Repeat with strong correlation among loci:
gbmc <- correlated.trees(pri10s, model="gbm", r=.04e-2, s2=.26e-2, 3, 0.9)
lapply(gbmc$trees, plot)

dosreislab/simclock documentation built on June 9, 2025, 11:57 p.m.