detachHookFromNode.PhyloSim: Detach a node hook function from a given node of a phylo...
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Value Author(s) See Also Examples

Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object.

1 2	## S3 method for class 'PhyloSim' detachHookFromNode(this, node=NA, ...)

`this`	A PhyloSim object.
`node`	Node identifier.
`...`	Not used.

The PhyloSim object (invisible).

Botond Sipos, Gregory Jordan

attachHookToNode PhyloSim Simulate.PhyloSim

	# Create a PhyloSim object.
	# Provide the phylo object
	# and the root sequence.
	sim<-PhyloSim(
		name="TinySim",
		phylo=rcoal(3),
		root.seq=NucleotideSequence(string="ATGC",processes=list(list(JC69())))
	);
	# create a node hook function
	hook<-function(seq=NA){
		# replace the substitution process with F84
		if(inherits(seq,"NucleotideSequence")){
			cat("Replacing JC69 with F84.\n");
			seq$processes<-list(list(F84(rate.params=list("Kappa" = 2))));
		}
		return(seq);
	}
	# attach hook function to node 5
	attachHookToNode(sim,5,hook);
	# detach hook from node 5
	detachHookFromNode(sim,5);
	# Run the simulation again
	Simulate(sim);	# You should not see the message printed out by the "hook" function.