Description Usage Arguments Details Value Note Author(s) See Also
runBatchHansen
estimates the support for character change on taxon-defined nodes, integrating over uncertainty in the phylogeny and the model of trait evolution.
1 2 3 |
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 tip-name 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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