Create a likelihood function of a numerical vector parameter

Create a likelihood function of a numerical vector parameter

PCMCreateLikelihood(
  X,
  tree,
  model,
  SE = matrix(0, PCMNumTraits(model), PCMTreeNumTips(tree)),
  metaI = PCMInfo(X, tree, model, SE),
  positiveValueGuard = Inf
)

Arguments

X	a k x N numerical matrix with possible NA and NaN entries. For i=1,..., N, the column i of X contains the measured trait values for species i (the tip with integer identifier equal to i in tree). Missing values can be either not-available (NA) or not existing (NaN). These two values 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 factor of the variance covariance matrix for the measurement error for each tip i=1, ..., N. When SE is a matrix, the k x k measurement error variance matrix for a tip i is calculated as VE[, , i] <- diag(SE[, i] * SE[, i], nrow = k). When SE is a cube, the way how the measurement variance matrix for a tip i is calculated depends on the runtime option PCMBase.Transpose.Sigma_x as follows: if getOption("PCMBase.Transpose.Sigma_x", FALSE) == FALSE (default): VE[, , i] <- SE[, , i] %*% t(SE[, , i]) if getOption("PCMBase.Transpose.Sigma_x", FALSE) == TRUE: VE[, , i] <- t(SE[, , i]) %*% SE[, , i] Note that the above behavior is consistent with the treatment of the model parameters Sigma_x, Sigmae_x and Sigmaj_x, which are also specified as upper triangular factors. 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. Alternatively, this can be a character string naming a function or a function object that returns such a list, e.g. the functionPCMInfo or the function PCMInfoCpp from the PCMBaseCpp package.
positiveValueGuard	positive numerical value (default Inf), which serves as a guard for numerical error. Values exceeding this positiveGuard are most likely due to numerical error and PCMOptions()$PCMBase.Value.NA is returned instead.

Value

a function of a numerical vector parameter called p returning the likelihood of X given the tree and the model with parameter values specified by p.

Details

It is possible to specify a function for the argument metaI. This function should have three parameters (X, tree, model) and should return a metaInfo object. (see PCMInfo).