runBatchHansen
estimates the support for character change on taxondefined nodes, integrating over uncertainty in the phylogeny and the model of trait evolution.
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ouchTrees 
A list of 
characterStates 
A vector of character states to analyze. As written, the function accepts a named vector, with names corresponding to tip names in the trees, a vector of length equal to the number of terminal branches, or a vector of length equal to the number of nodes in the trees 
cladeMembersList 
A list of tipname vectors, each defining a node of interest in the tree. Because these vectors are checked for monophyly on each tree, each node must by defined by all tips descendent from that node 
filePrefix 
A file prefix for saving hansen objects. If left at default ( 
di 
A directory in which to save hansen objects. Not required, but strongly recommended if you are saving hansen objects. 
nodeNames 
A vector of names for the nodes being analyzed. Not implemented. 
maxNodes 
The maximum number of nodes at which the regime is allowed to change. Defaults to the number of nodes specified. 
regimeTitles 
Names for regimes; only enter if you know how many regimes you will be getting and have reason to name them. Optional. 
brown 
Enter 
... 
Arguments passed along to 
This function is the primary function for estimating the probability of a change in with changes in regime at the nodes specified, with changes corresponding to permutations of the nodes fed to the function. See vignette for additional details.
A list of class hansenBatch
with the following items:
hansens 
A matrix with rows equal to the number of models analyzed, and four columns:

thetas 
A list of vectors with a 
regList 
A list indexed by tree of lists indexed by model, with the regime corresponding to each model on each tree. 
regMatrix 
The nodes by regimes matrix returned by 
nodeMatrix 
A nodes by tree matrix, indicating for each tree which nodes are present. 
brown 
A boolean vector of length one indicating whether the brownian motion model was fitted. 
N 
The sample size (number of terminals on the trees). 
analysisDate 
Data of analysis. 
call 
Verbatim call to 
Summary estimates of the probability of change on a branch are only valid if (1) the maximum number of regimes permitted approximates the actual maximum; (2) nodes at which changes actually occurred were included among the nodes being tested; and (3) any matrix you may have utilized to conduct analysis was balanced, such that all nodes are present in the same number of models.
Andrew Hipp <ahipp@mortonarb.org>
summary.hansenBatch
for summarizing data; carex
for an example
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