R: Generate a list of model setups for the function...
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.
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".
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.