Context of a MCMC

Context of a MCMC

MCMCContext(X, tree, model, SE = matrix(0, PCMNumTraits(model),
  PCMTreeNumTips(tree)))

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	a template used to build MixedGaussian model objects.
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 node i=1, ..., N. Default: matrix(0.0, PCMNumTraits(model), PCMTreeNumTips(tree)).

Value

an object of S3 class 'MCMCContext'.