mlogl.Rd
\name{mlogl}
\alias{mlogl}
\title{Minus Log Likelihood for Aster Models}
\usage{
mlogl(parm, pred, fam, x, root, modmat, deriv = 0,
type = c("unconditional", "conditional"), famlist = fam.default(),
origin, origin.type = c("model.type", "unconditional", "conditional"))
}
\description{
Minus the Log Likelihood for an Aster model, and its first and second
derivative. This function is called inside \code{\link{aster}}.
Users generally do not need to call it directly.
}
\arguments{
\item{parm}{parameter value (vector of regression coefficients)
where we evaluate the log likelihood, etc.
We also refer to \code{length(parm)} as \code{ncoef}.}
\item{pred}{integer vector determining the graph.
\code{pred[j]} is the index of the predecessor of
the node with index \code{j} unless the predecessor is a root
node, in which case \code{pred[j] == 0}.
We also refer to \code{length(pred)} as \code{nnode}.}
\item{fam}{an integer vector of length \code{nnode} determining
the exponential family structure of the aster model. Each element
is an index into the vector of family specifications given by
the argument \code{famlist}.}
\item{x}{the response. If a matrix, rows are individuals, and columns are
variables (nodes of graphical model). So \code{ncol(x) == nnode} and
we also refer to \code{nrow(x)} as \code{nind}. If not a matrix, then
\code{x} must be as if it were such a matrix and then dimension
information removed by \code{x = as.numeric(x)}.}
\item{root}{A matrix or vector like \code{x}.
Data \code{root[i, j]} is the data for the founder that is
the predecessor of the response \code{x[i, j]}
and is ignored when \code{pred[j] > 0}.}
\item{modmat}{a three-dimensional array, \code{nind} by \code{nnode} by
\code{ncoef}, the model matrix. Or a matrix, \code{nind * nnode} by
\code{ncoef} (when \code{x} and \code{root} are one-dimensional
of length \code{nind * nnode}).}
\item{deriv}{derivative wanted: 0, 1, or 2.}
\item{type}{type of model. The value of this argument can be abbreviated.}
\item{famlist}{a list of family specifications (see \code{\link{families}}).}
\item{origin}{Distinguished point in parameter space. May be missing,
in which case an unspecified default is provided. See \code{\link{aster}}
for further explanation.}
\item{origin.type}{Parameter space in which specified distinguished point
is located. If \code{"conditional"} then argument \code{"origin"} is
a conditional canonical parameter value.
If \code{"unconditional"} then argument \code{"origin"} is
an unconditional canonical parameter value.
If \code{"model.type"} then the type is taken from argument \code{"type"}.
The value of this argument can be abbreviated.}
}
\value{
a list containing some of the following components:
\item{value}{minus the log likelihood.}
\item{gradient}{minus the first derivative vector of the log likelihood
(minus the score).}
\item{hessian}{minus the second derivative matrix of the log likelihood
(observed Fisher information).}
}
\keyword{misc}