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