fp.comp.subs: FP.comp.subs

In iteRates: Parametric rate comparison

Description

This function simulates pure birth trees with a given number of taxa and NA subtrees and calculates the null expectation for the number of significant rate differences.

Usage

FP.comp.subs(tree.size, na.present, sims = 100, missing = 0, 
alpha = 0.05, verbose = FALSE, ...)

Arguments

tree.size	A value for the number of terminal taxa in the tree to simulate.
na.present	A value for the number of NA subtrees in the simulated trees.
sims	A value for the number of trees to simulate.
missing	A value indicating the number of missing taxa from the tree.
alpha	A value indicating the threshold for statistical significance.
verbose	A boolean indicating whether a summary of the simulations is printed to the screen.
...	Arguments passed on to comp.subs function

Details

This function is useful if the user wants to know the expected number of significant rate differences for a tree of a given size and number of NA subtrees. This function calls on comp.subs, and arguments can be passed on.

Value

A list that consists of the following:

tree.size	The number of terminal taxa provided by the user.
missing	The number of missing taxa from the tree.
sims	The number of simulated trees.
FPRthres	The number of significant rate difference detections expected based upon the alpha value provided by the user.

Note

comp.subs is an exploratory data analysis tool and concerns of false positives should be considered accordingly. The argument "missing" can be used for trees with incomplete taxon sampling. Thus, if a group should have 100 taxa included, but only 90 are present in the tree, tree.size=100 and missing=10.

Author(s)

Premal Shah, Benjamin Fitzpatrick and James Fordyce.

References

Shah, P., B. M. Fitzpatrick, and J. A. Fordyce. 2013. A parametric method for assessing diversification rate variation in phylogenetic trees. Evolution 67:368-377.

See Also

comp.subs

Examples

	## Not run: 
data(geospiza)
tree<-geospiza$geospiza.tree
na.count<-tree.na.Count(tree)
FP.comp.subs(tree.size=14,na.present=na.count,verbose=TRUE)

## End(Not run)

iteRates documentation built on May 2, 2019, 9:12 a.m.