PCMInfoCpp: A S3 generic for creating C++ backend objects given a model,...

In PCMBaseCpp: Fast Likelihood Calculation for Phylogenetic Comparative Models

A S3 generic for creating C++ backend objects given a model, data and a tree.

Description

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

Usage

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,
  ...
)

Arguments

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.

Value

a list to be passed to PCMLik as argument metaI.

Examples

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)

PCMBaseCpp documentation built on June 8, 2025, 11:19 a.m.