simulate.clock: simulate.clock

In sebastianduchene/NELSI: NELSI: Nucleotide EvoLution Simulator

simulate.clock

Description

simulate.clock simulates a constant rate of evolution along a phylogenetic tree

Usage

simulate.clock(tree, params = list(rate = 0.006, noise = 0.00001))

Arguments

tree	A phylogeneti tree of class 'phylo'. The tree should be a chronogram, with branch lengths in time.
params	parameters for the clock rate simulation function. This should be a list with two items:
rate	The rate for the tree
noise	The stochastic noise. Note that if this parameter is set very high compared to the rate, the model will be similar to an uncorrelated rates model

Details

None

Value

An object of class 'ratesim'. This is a list with two items:

phylogram	The phylogenetic tree with branch lengths in units of substitutions (phylogram)
tree.data.matrix	This is a matrix with the number of substitutions, rates, and times along every branch in the tree. See get.tree.data.matrix for more details

Note

None

Author(s)

Sebastian Duchene. See references for the original description of the molecular clock.

References

This is a constant molecular rate model. The original model can be found in: Zuckerkandl, Emile, and Linus Pauling. "Molecular disease, evolution and genetic heterogeneity." (1962): 189-225.

Zuckerkandl, Emile, and Linus Pauling. "Evolutionary divergence and convergence in proteins." Evolving genes and proteins 97 (1965): 97-166.

See Also

None.

Examples

set.seed(1234525)

myTree <- rcoal(10)

# A tree with low stochastic variation
rateClock <- simulate.clock(tree = myTree, params = list(rate = 0.006, noise = 0.00001))

#Note the scale in the y axis. Rate variation is very low
plot(rateClock, col.lineages = rainbow(10))


## The function is currently defined as
function (tree, params = list(rate = 0.006, noise = 0.00001)) 
{
    rate <- params$rate
    noise <- params$noise
    data.matrix <- get.tree.data.matrix(tree)
    branch.rates <- rep(rate, times = length(tree$edge.length))
    branch.rates <- abs(branch.rates + rnorm(length(tree$edge.length), 
        mean = 0, sd = noise))
    data.matrix[, 5] <- branch.rates
    data.matrix[, 6] <- data.matrix[, 5] * data.matrix[, 7]
    tree$edge.length <- data.matrix[, 6]
    res <- list(tree, data.matrix)
    names(res) <- c("phylogram", "tree.data.matrix")
    class(res) <- "ratesim"
    return(res)
  }

sebastianduchene/NELSI documentation built on Sept. 5, 2024, 3:08 a.m.