An S3 generic function that has to be implemented for every
model class. This function is called by PCMLik
.
PCMAbCdEf(tree, model, SE = matrix(0, PCMNumTraits(model),
PCMTreeNumTips(tree)), metaI = PCMInfo(NULL, tree, model, verbose =
verbose), verbose = FALSE)
a phylo object with N tips.
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).
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 node i=1, ..., N.
Default: matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))
.
a list returned from a call to PCMInfo(X, tree, model, SE)
,
containing meta-data such as N, M and k. Alternatively, this can be a
function object that returns such a list, e.g. the functionPCMInfo
or the function PCMInfoCpp
from the PCMBaseCpp
package.
logical indicating if some debug-messages should printed.