This is an S3 generic function providing tracing information for the likelihood calculation for a given tree, data and model parameters. Useful for illustration or for debugging purpose.
PCMLikTrace(X, tree, model, SE = matrix(0, PCMNumTraits(model),
PCMTreeNumTips(tree)), metaI = PCMInfo(X = X, tree = tree, model =
model, SE = SE, verbose = verbose), log = 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 a log-likelehood should be calculated. Default is TRUE.
logical indicating if some debug-messages should printed.
The returned object will, in general, depend on the type of model and the algorithm used for likelihood calculation. For a G_LInv model and pruning-wise likelihood calculation, the returned object will be a data.table with columns corresponding to the node-state variables, e.g. the quadratic polynomial coefficients associated with each node in the tree.
PCMInfo
PCMAbCdEf
PCMLmr
PCMSim
PCMCond
PCMParseErrorMessage