simulate.rate: simulate.rate is the generic function to simulate rates along...
In sebastianduchene/NELSI: NELSI: Nucleotide EvoLution Simulator

simulate.rate

R Documentation

simulate.rate is the generic function to simulate rates along phylogenetic trees with any of the models.

Description

simulate.rate simulates the rate with any of the models implemented in NELSI

Usage

simulate.rate(tree, FUN, ...)

Arguments

`tree`	A phylogenetic tree of class 'phylo'. The branch lengths should be in units of time (a chronogram)
`FUN`	This is any of the rate simulation functions (please see the help for each for details on the models): - simulate.autocor.kishino - simulate.autocor.thorne - simulate.clock - simulate.tdep.generic - simulate.tdep.ho - simulate.uncor.exp - simulate.uncor.lnorm - simulate.uncor.gamma - simulate.white.noise
`...`	This should be the parameters for the rate models. To specify this use: params = list(parameter1 , parameter2). See the help files for each rate simulation function for details on the parameters.

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)

David Duchene and Sebastian Duchene

References

See the original reference for NELSI: Pending.

Examples

set.seed(1234525)

myTree <- rcoal(50)

# Simulate uncorrelated rates with default parameters:
rateTree.default <- simulate.rate(tree = myTree, FUN = simulate.uncor.lnorm)
plot(rateTree.default, col.lineages = rainbow(50))

# Simulate uncorrelated rates with custom parameters:
rateTree.custom <- simulate.rate(tree = myTree, FUN = simulate.uncor.lnorm, params = list(mean.log = -3.9, sd.log = 0.8))
plot(rateTree.custom, col.lineages = rainbow(50))


## The function is currently defined as
function (tree, FUN, ...) 
{
    ratesim.object <- FUN(tree, ...)
    return(ratesim.object)
  }

sebastianduchene/NELSI documentation built on Aug. 18, 2022, 11:45 p.m.