PCMLmr {PCMBase}

Quadratic polynomial parameters L, m, r

Description

Quadratic polynomial parameters L, m, r

Usage

PCMLmr(
  X,
  tree,
  model,
  SE = matrix(0, PCMNumTraits(model), PCMTreeNumTips(tree)),
  metaI = PCMInfo(X = X, tree = tree, model = model, SE = SE, verbose = verbose),
  root.only = TRUE,
  verbose = FALSE
)

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.

root.only

logical indicating whether to return the calculated values of L,m,r only for the root or for all nodes in the tree.

verbose

logical indicating if some debug-messages should printed.

Value

A list with the members A,b,C,d,E,f,L,m,r for all nodes in the tree or only for the root if root.only=TRUE.