Quadratic polynomial parameters L, m, r

PCMLmr(X, tree, model, metaI = PCMInfo(X, tree, model, verbose =
  verbose), root.only = TRUE, verbose = FALSE)

Arguments

X

a k x N numerical matrix with possible NA and NaN entries. Each column of X contains the measured trait values for one species (tip in tree). Missing values can be either not-available (NA) or not existing (NaN). Thse two values have are treated differently when calculating likelihoods: see PCMPresentCoordinates.

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).

metaI

a list returned from a call to PCMInfo(X, tree, model), containing meta-data such as N, M and k.

root.only

logical indicatin whether to return the calculated values of L,m,r only for the root or for all nodes in the tree.

verbose

logical indicating if some debug-messages should printed.

Value

A list with the members A,b,C,d,E,f,L,m,r for all nodes in the tree or only for the root if root.only=TRUE.