R/ml.loglik.gr.R

In gasparrini/mixmeta: An Extended Mixed-Effects Framework for Meta-Analysis

###
### R routines for the R package mixmeta (c)
#
ml.loglik.gr <-
function(par, Xlist, Zlist, ylist, Slist, nalist, rep, k, q, nall, const,
  bscov, fix) {
#
################################################################################
#
  # COMPUTE Psi FROM PARAMETERS
  # NB: GRADIENT ONLY AVAILABLE FOR SINGLE-LEVEL AND UNSTRUCTURED RANDOM
  L <- diag(0,k)
  L[lower.tri(L, diag = TRUE)] <- par
  U <- t(L)
  Psi <- crossprod(U)
#
  # FIT BY GLS
  Sigmalist <- getSigmalist(NULL,nalist,Psi,Slist)
  gls <- glsfit(Xlist,ylist,Sigmalist,onlycoef=FALSE)
#
  # COMPUTE QUANTITIES
  invSigmalist <- lapply(gls$invUlist,tcrossprod)
  reslist <- mapply(function(X,y) as.numeric(y-X%*%gls$coef),
    Xlist,ylist,SIMPLIFY=FALSE)
  ind1 <- rep(1:k,k:1)
  ind2 <- unlist(sapply(1:k,seq,to=k))
#
  # RETURN
  gradchol.ml(par,U,ind1,ind2,invSigmalist,reslist,nalist,k)
}