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This function will trim a specified amount of time, or branch length, from the tips of an ultrametric tree.
● Data Source:
CranContrib
● Keywords:
● Alias: trimTree
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This function performs a randomization test for rate variation among clades.
● Data Source:
CranContrib
● Keywords:
● Alias: tree.rand.test
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This function will identify the number of NA subtrees present in a given phylogenetic tree.
● Data Source:
CranContrib
● Keywords:
● Alias: tree.na.Count
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This function provides an abridged output of results obtained from the comp.fit.subs function by restricting the output to a user provided delta AIC threshold.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: tab.summary
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Iterates through a phylogenetic tree to identify regions of rate variation using the parametric rate comparison test.
● Data Source:
CranContrib
● Keywords:
● Alias: iteRates, iteRates-package
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This function identifies and numbers all subtrees within a tree of object class phylo. It creates the object required for function comp.fit.subs.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: id.subtrees
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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.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: FP.comp.subs
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The function implements the parametric rate comparison test. The function iterates through all subtrees of a phylogenetic tree and compares the distribution of branch lengths in the subtree to the "remainder" tree. It is intended to be used with a chronogram in order to test whether diversification rates differ among clades within a broader phylogeny. A variety of truncated distributions can be used and compared via likelihood.
● Data Source:
CranContrib
● Keywords:
● Alias: comp.subs
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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.
● Data Source:
CranContrib
● Keywords: ~kwd1, ~kwd2
● Alias: comp.fit.subs
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This function plots phylogenetic trees on the current graphical device and indicates potential regions of the tree that might have undergone a shift in diversification rate.
● Data Source:
CranContrib
● Keywords:
● Alias: color.tree.plot
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providing 
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