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 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.
a k x N
numerical matrix with possible NA
and
NaN
entries. For i=1,..., N
, the column i
of X contains
the measured trait values for species i
(the tip with integer
identifier equal to i
in tree
). Missing values can be either
not-available (NA
) or not existing (NaN
). These two values 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 tip i=1, ..., N
. When SE
is a matrix, the k x k
measurement error variance matrix for a tip i
is calculated as
VE[, , i] <- diag(SE[, i] * SE[, i], nrow = k)
. When SE
is a
cube, the way how the measurement variance matrix for a tip i
is
calculated depends on the runtime option PCMBase.Transpose.Sigma_x
as follows:
getOption("PCMBase.Transpose.Sigma_x", FALSE) == FALSE
(default): VE[, , i] <- SE[, , i] %*% t(SE[, , i])
getOption("PCMBase.Transpose.Sigma_x", FALSE) == TRUE
: VE[, , i] <- t(SE[, , i]) %*% SE[, , i]
Note that the above behavior is consistent with the treatment of the model
parameters Sigma_x
, Sigmae_x
and Sigmaj_x
, which are
also specified as upper triangular factors.
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
character string naming a function or 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.