PCMLikTrace | R Documentation |
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
)
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). |
SE |
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
Note that the above behavior is consistent with the treatment of the model
parameters |
metaI |
a list returned from a call to |
log |
logical indicating whether a log-likelehood should be calculated. Default is TRUE. |
verbose |
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
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