PCMInfoCpp: A S3 generic for creating C++ backend objects given a model,...
In PCMBaseCpp: Fast Likelihood Calculation for Phylogenetic Comparative Models

Description Usage Arguments Value Examples

Replace calls to PCMInfo() with this method in order to use C++ for likelihood calculation.

PCMInfoCpp(X, tree, model, SE = matrix(0, PCMNumTraits(model),
  PCMTreeNumTips(tree)), metaI = PCMInfo(X = X, tree = tree, model =
  model, SE = SE, verbose = verbose, preorder = PCMTreePreorderCpp(tree)),
  verbose = FALSE, ...)

`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`). These 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).
`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 Choleski factor of the variance covariance matrix for the measurement error for each node i=1, ..., N. Default: `matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree))`.
`metaI`	a list returned from a call to `PCMInfo(X, tree, model, SE)`, containing meta-data such as N, M and k. Default: `PCMInfo(X, tree, model, verbose, preorder=PCMTreePreorderCpp(tree))`
`verbose`	logical indicating if some debug-messages should be printed. Default: FALSE
`...`	passed to methods.

a list to be passed to PCMLik as argument metaI.

metaICpp <- PCMInfoCpp(
PCMBase::PCMBaseTestObjects$traits.a.123, 
PCMBase::PCMBaseTestObjects$tree.a,
PCMBase::PCMBaseTestObjects$model.a.123)
PCMBase::PCMLik(
PCMBase::PCMBaseTestObjects$traits.a.123, 
PCMBase::PCMBaseTestObjects$tree.a,
PCMBase::PCMBaseTestObjects$model.a.123,
metaI = metaICpp)