simARG {ARG}R Documentation

Simulate an ancestral recombination graph

Description

Simulate an ancestral recombination graph. The

Usage

simARG(ss,sites,rec,growthmodel="constant",migmatrix,poptree)

Arguments

ss Sample size - either a vector or number
sites Number of sites between which recombination can occur
rec Recombination rate between sites, either a simgle number or an array of length sites-1
growthmodel growth model, e.g. "constant" or "exponential(2)"
migmatrix The migration matrix. Either an actual matrix or a string such as "Island(4,1)" that indicates an island model for 4 populations with a migration rate of 1 individual per generation
poptree A population tree - a string in Newick format. Assumes a single population if missing.

Details

Value

The data is not stored within R, rather it is allocated within a static data structure within the C code, and information about it is extracted using R functions. The list contains information about where it is stored in R, so that multiple structures may be stored. A list is produced with the some or all of the components:

ss The sample size
sites The nuimber of sites sampled
rec The recombination rate between sites
wh A label that gives which ARG this is (for internal package use)
growthmodel The growthmodel used for simulation
location A vector of the locations of samples
migmatrix The migration matrix used

Warning

The Ancestral Recombination Graph structures may take up a large amount of memory with large recombination rates. If you want to use many large structures it is best to use ARG.remove to remove unwanted structures.

Author(s)

Ian Wilson <I.J.Wilson@ncl.ac.uk>

References

The newick tree format: http://evolution.genetics.washington.edu/phylip/newicktree.html

See Also

treelength treeheight ARG.remove

Examples

a <- simARG(ss=100,sites=1000,rec=0.1)
b <- simARG(ss=100,sites=1000,rec=0.1,growthmodel="exponential(1)")
plot(treeheight(a),type="l",ylim=c(0,10));
lines(treeheight(b),col="blue");

[Package ARG version 0.1 Index]