sample.tree: Sample a coalescent tree according to a PCR experiment

In pcrcoal: Implementing the Coalescent Approach to PCR Simulation Developed by Weiss and Von Haeseler (NAR, 1997)

Description

This method returns a coalescent tree sampled according to the PCR experiment specified by the parameters stored in the slots of the PCRcoal object given as the first argument. All of the slots must contain a defined value.

Use this method if you are interested only in the sampled tree.

Usage

	## S4 method for signature 'PCRcoal'
sample.tree(object)

Arguments

object

A PCRcoal object, with all the slots defined.

Value

An ape phylo object (rooted).

See Also

The PCRcoal class. The sample.tnt and sample.trs methods.

Examples

	# Construct a PCRcoal object 
	# and specify the experimental conditions:
	sim <-PCRcoal(
        initial.size    =5,
        sample.size     =10,
        nr.cycles       =30,
        efficiencies    =c(rep(0.1, 30))
    	)

	# Sample a coalescent tree:
	tree <- sample.tree(sim)

	# Print tree info:
	print(tree)

	# Plot the tree:
	plot(tree)
	

pcrcoal documentation built on May 1, 2019, 8:03 p.m.