Rsampletrees (version 0.1)

treeapply: Apply a function to the sampled trees

Description

This function is used to apply a user-supplied function to each tree that was sampled in a run of sampletrees.

Usage

treeapply(output, myfunc, funcname=NULL, maxlines=1000, treerange=NULL)

Arguments

output

An object of class `treeoutput'

myfunc

The function to be applied to each tree

funcname

The name of the function to be used for the column name of the data frame that is returned

maxlines

The maximum number of lines of the tree file to read in at a time. This avoids large tree files from fully being read in.

treerange

A vector giving the indices of the trees to which the function should be applied. Only used if the trees are not stored in the treeoutput object

Value

Details

This function is meant to be similar to the various `apply' functions, such as lapply and sapply, in that it can be used to apply a function to each elements of a list or vector. In this case, it applies the specified function to an object of class 'multiPhylo', which is a list of trees.

The trees to apply the function to are found in the rawdata component of the treeoutput object (either the tree file name or the trees stored as an object of class `multiPhylo').

The function must be written to manipulate tree data of type 'phylo'. See the 'ape' package documentation for more information about the format of tree data.

References

TBD

See Also

addTreeStats

Examples

mrca.age=function(tree)
{
	return(coalescent.intervals(tree)$total.depth)
}

filename=system.file("Examples/example_g_pars", package="Rsampletrees")
runpars=readArgs(filename, check=FALSE)

# Must change the path so that the output can be found
runname=paste(system.file(package="Rsampletrees"),runpars$RunName, sep="/")
runpars=changeArgs(runpars, RunName=runname)

# Read in the output
results=readOutput(argob=runpars, addtrees=TRUE)
test=treeapply(results, myfunc=mrca.age,funcname="TimeMRCA")

results=readOutput(argob=runpars)
test=treeapply(results, myfunc=mrca.age, treerange=50:60)