This function pre-processes the given tree and data in order to create meta-information used during likelihood calculaiton.
PCMInfo(X, tree, model, verbose = FALSE, preorder = NULL, ...)
X | a |
---|---|
tree | a phylo object with N tips. |
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). |
verbose | logical indicating if some debug-messages should printed. |
preorder | an integer vector of row-indices in tree$edge matrix as returned
by PCMTreePreorder. This can be given for performance speed-up when several
operations needing preorder are executed on the tree. Default : |
... | additional arguments used by implementing methods. |
a named list with the following elements:
total number of nodes in the tree;
number of tips;
number of traits;
number of regimes on the tree (distinct elements of tree$edge.regime);
number of regimes in the model (distinct elements of attr(model, regimes));
number of free parameters describing the model;
an integer vector corresponding to tree$edge with the regime for each branch in tree;
an integer vector of 0's and 1's corresponding to the rows in tree$edge indicating the presence of a jump at the corresponding branch;
a logical matrix of dimension k x M denoting the present coordinates for each node;