Summarize output from runBatchHansen

Description

summary.hansenBatch is a summary method for a hansenBatch object. print.hansenSummary is a print method for a hansenSummary object.

Usage

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  ## S3 method for class 'hansenBatch'
summary(object, ic = 'AICc', ...)
  ## S3 method for class 'hansenSummary'
print(x, ...)

Arguments

object

Output from runBatchHansen.

ic

Choice of information criterion to use in model-averaging of parameters. Choices are AICc (default), AIC, or BIC.

x

Output from summary.hansenBatch.

...

Additional arguments to print or summary.

Details

summary.hansenBatch averages parameters over models and over trees, and provides the cumulative information-criterion weight for models containing each node as an estimate of the support for the hypothesis that there was a character shift at that node. print.hansenSummary provides an easy-to-read synopsis of the analysis summary. Called automatically when you simply type in the name of the summary object.

Value

For summary.hansenBatch, a list of class hansenSummary with the following items:

modelsMatrix

A list of matrices, indexed by tree, providing the information criterion weights for each model.

nodeWeightsMatrix

A list of length two with two matrices:

  • unnormalized The cumulative information criterion weight for each node, averaged only over trees that possess that node

  • allNodes The cumulative information criterion weight for each node, averaged over all trees.

modelAvgAlpha

The model-averaged estimate of alpha, the rate of evolution toward the equilibrium / optimum

modelAvgSigmaSq

The model-averaged estimate of sigma.squared, the variance or rate of stochastic evolution.

thetaMatrix

A matrix with trees as the rows, branch number as the columns, containing the model-averaged value of theta (the character equilibrium or optimum value) for each branch on each tree

Author(s)

Andrew Hipp ahipp@mortonarb.org

See Also

carex for an example