summary.hansenBatch: Summarize output from runBatchHansen

In maticce: Mapping Transitions in Continuous Character Evolution

Description

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

Usage

  ## 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 [e-mail]

See Also

carex for an example

maticce documentation built on May 2, 2019, 6:13 p.m.