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PCMAbCdEf.Rd
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PCMAbCdEf.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/GaussianPCM.R
\name{PCMAbCdEf}
\alias{PCMAbCdEf}
\title{Quadratic polynomial parameters A, b, C, d, E, f for each node}
\usage{
PCMAbCdEf(
tree,
model,
SE = matrix(0, PCMNumTraits(model), PCMTreeNumTips(tree)),
metaI = PCMInfo(NULL, tree, model, verbose = verbose),
verbose = FALSE
)
}
\arguments{
\item{tree}{a phylo object with N tips.}
\item{model}{an S3 object specifying both, the model type (class, e.g. "OU") as
well as the concrete model parameter values at which the likelihood is to be
calculated (see also Details).}
\item{SE}{a k x N matrix specifying the standard error for each measurement in
X. Alternatively, a k x k x N cube specifying an upper triangular k x k
factor of the variance covariance matrix for the measurement error
for each tip \code{i=1, ..., N}. When \code{SE} is a matrix, the k x k
measurement error variance matrix for a tip \code{i} is calculated as
\code{VE[, , i] <- diag(SE[, i] * SE[, i], nrow = k)}. When \code{SE} is a
cube, the way how the measurement variance matrix for a tip \code{i} is
calculated depends on the runtime option \code{PCMBase.Transpose.Sigma_x}
as follows:
\describe{
\item{if \code{getOption("PCMBase.Transpose.Sigma_x", FALSE) == FALSE} (default): }{VE[, , i] <- SE[, , i] \%*\% t(SE[, , i])}
\item{if \code{getOption("PCMBase.Transpose.Sigma_x", FALSE) == TRUE}: }{VE[, , i] <- t(SE[, , i]) \%*\% SE[, , i]}
}
Note that the above behavior is consistent with the treatment of the model
parameters \code{Sigma_x}, \code{Sigmae_x} and \code{Sigmaj_x}, which are
also specified as upper triangular factors.
Default: \code{matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))}.}
\item{metaI}{a list returned from a call to \code{PCMInfo(X, tree, model, SE)},
containing meta-data such as N, M and k. Alternatively, this can be a
character string naming a function or a function object that returns such
a list, e.g. the function\code{PCMInfo} or the function \code{PCMInfoCpp}
from the \code{PCMBaseCpp} package.}
\item{verbose}{logical indicating if some debug-messages should printed.}
}
\description{
An S3 generic function that has to be implemented for every
model class. This function is called by \code{\link{PCMLik}}.
}