comp.fit.subs: comp.fit.subs

In iteRates: Parametric rate comparison

Description

The function implements the K-clades parametric rate comparison test. This function compares rate estimates among defined subtrees and evaluates various groupings from 1 to k groups for these subtrees.

Usage

comp.fit.subs(trees, focal, k, mod.id = c(1, 0, 0, 0), min.val = 0.01)

Arguments

trees	A list from from function id.subtrees.
focal	A vector indicating the subtrees to compare
k	A value indicting the maximum number of groupings of subtrees to examine
mod.id	A vector with four elements of 0 or 1 indicating which models to consider. 1 indicates that the model should be considered. 0 indicates the model is not considered. These for elements refer to an exponential, Weibel, lognormal, and rate variable, respectively.
min.val	A value for determining the minimum edge length for a tree scaled against the longest edge length. A value of 0.01 (the default) rescales the minimum edge length to 1

Details

The list of possible subtrees is provided by the function id.subtrees. The function will explore all possible groupings of subtrees into k defined groups choosing the best fit model for each partition from among the models identified by mod.id.

Value

A dataframe that consists of the following:

k	The number of groups
Groups	The groupings for each subtree numbered as 1 to the number of subtrees indicated. The numbering corresponds to the order in which subtrees are identified by focal. Groups are separated with vs.
gi_Pj	The jth parameter value for the ith group in the analysis
gi_mod.id	The best model chosen for the ith group
gi_n.param	The number of parameters in the best model for the ith group
AIC	Akaike information criterion score for the entire model for a grouping scheme
AICc	Akaike information criterion corrected for sample size
dAICc	The delta AIC across all grouping schemes and k values relative to the best fit model

Note

The output can get very large as k increases. Function tab.summary is useful for reducing the size of the result table.

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

tab.summary id.subtrees

Examples

data(hivtree.newick)
cat(hivtree.newick, file = "hivtree.phy", sep = "\n") 
tree.hiv <- read.tree("hivtree.phy") # load tree 
unlink("hivtree.phy") # delete the file "hivtree.phy" 

idHIV<-id.subtrees(tree.hiv)
plot(idHIV$tree,show.node.label=TRUE)
cfsHIV<-comp.fit.subs(idHIV$subtree,focal=c(153,119,96,5),k=4)

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