generate.model.setups: Generate a list of model setups for the function...
In mvSLOUCH: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

generate.model.setups

R Documentation

Generate a list of model setups for the function `estimate.evolutionary.model`.

Description

The function generates a list of models that will be used by the function
estimate.evolutionary.model. A minimum example list will be list(list(evolmodel="bm")).

Usage

generate.model.setups()

Details

The function should really be a hidden one but is left available for the user as an example how such a list of models should be generated.

The setting Atype="Any" means that one assumes the matrix A is eigendecomposable. If A is defective, then the output will be erroneous.

None of the "signs" options for the model is generated, see the description of mvslouchModel and ouchModel.

Value

A list with different models is returned. Each element of the list is a list with the following fields.

evolmodel: The evolutionary model, it may take one of the three values "BM" (Brownian motion model), "ouch" (OUOU model), "mvslouch" (OUBM model).
Atype: The class of the A matrix, ignored if evolmodel equals "BM". Otherwise it can take one of the following values: "SingleValueDiagonal", "Diagonal", "UpperTri", "LowerTri", "SymmetricPositiveDefinite", "Symmetric", "DecomposablePositive",
"DecomposableNegative", "DecomposableReal", "Invertible", "TwoByTwo", "Any".
Syytype: The class of the A matrix, ignored if evolmodel equals "BM". Otherwise it can take one of the following values: "SingleValueDiagonal", "Diagonal", "UpperTri", "LowerTri", "Symmetric", "Any".
diagA: Should the diagonal of A be forced to be positive (TRUE), negative (FALSE) or the sign free to vary (NULL)

Author(s)

Krzysztof Bartoszek

References

Bartoszek, K. and Pienaar, J. and Mostad. P. and Andersson, S. and Hansen, T. F. (2012) A phylogenetic comparative method for studying multivariate adaptation. Journal of Theoretical Biology 314:204-215.