Tentative formal rules for definition of corrFamily descriptors (work in progress). This is likely to repeat and extend information partially given in corrFamily and corrFamily-design documentations.
User-level rules (not relevant fo corrFamily descriptors internally modified during a fit):
Should always be present. For trivial parameterless cases (e.g. ranGCA), it should be numeric(0L), not NULL.
function; should always be present. For trivial uncorrelated random effects (e.g. ranGCA,
where only the Af function carries the information for the model),
it should return an identity matrix, not NULL,
with row names to be matched to the column names of the Z matrix for the random effect.
optional function. If present, it should have formal arguments including at least corrfamily and ....
function; optional. If present, it should have row names to be matched to the column names of the Z matrix for the random effect, and also needs column names if it is to be matched with the row names of a correlation matrix (or its inverse).
Optional function. If present, should have formal arguments including at least Zmatrix and ....
In predefined corrFamily constructors, variables created by initialize for use by Cf or Af should be declared (typically as NULL) in the body of the constructor, so that R CMD check does not complain.
An environment. initialize may write into it. It might also read into it, for example read the result of a long previous computation by initialize during a previous fit, though this opens the door to various errors.