Quadratic polynomial parameters L, m, r
PCMLmr(X, tree, model, SE = matrix(0, PCMNumTraits(model),
PCMTreeNumTips(tree)), metaI = PCMInfo(X = X, tree = tree, model =
model, SE = SE, verbose = verbose), root.only = TRUE,
verbose = FALSE)
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
).
These two values have are treated differently when calculating
likelihoods: see PCMPresentCoordinates
.
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 whether to return the calculated values of L,m,r only for the root or for all nodes in the tree.
logical indicating if some debug-messages should printed.
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.