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# General function that forms the model matrices
formModelMatrices <- function(x){
# x is the model:
pars <- x@parameters
mats <- x@matrices
# All groups:
allGroups <- x@sample@groups$id
nGroup <- length(allGroups)
# form matrices:
Matrices <- lapply(seq_len(nGroup),function(g){
groupMod <- lapply(seq_len(nrow(mats)),function(i){
# For incomplete, use NA, otherwise 0
if (mats$incomplete[i]){
mat <- matrix(NA, mats$nrow[i], mats$ncol[i])
} else {
mat <- matrix(0, mats$nrow[i], mats$ncol[i])
}
for (id in which(pars$matrix==mats$name[i]&pars$group_id==g)){
mat[pars$row[id],pars$col[id]] <- pars$est[id]
}
if (mats$symmetrical[i]){
mat[upper.tri(mat)] <- t(mat)[upper.tri(mat)]
}
# What kind of matrix?
# if (mats$diagonal[i]){
# mat <- as(mat, "diagonalMatrix")
#
# } else if (mats$lowertri[i]){
# mat <- as(mat, "Matrix")
# } else if (mats$sparse[i]){
# if (mats$symmetrical[i]){
# mat <- as(mat, "dsCMatrix")
# } else {
# mat <- as(mat, "sparseMatrix")
# }
# } else if (mats$posdef[i]){
# mat <- as(mat, "dpoMatrix")
# } else if (mats$symmetrical[i]){
# mat <- as(mat, "dsyMatrix")
# } else {
# mat <- as(mat, "dgeMatrix")
# }
# if (mats$diagonal[i]){
# mat <- Diagonal(x=diag(mat))
# } else if (mats$sparse[i]){
#
# if (mats$symmetrical[i]){
# mat <- as(mat, "dsCMatrix") # symmetric column-oriented numeric sparse matrix
# } else {
# mat <- as(mat, "dMatrix") # general column-oriented numeric sparse matrix
# }
#
# }
# if (mats$diagonal[i]){
# mat <- Diagonal(x=diag(mat))
# } else {
mat <- as.matrix(mat)
# }
# mat <- as(mat, "Matrix")
mat
})
names(groupMod) <- mats$name
groupMod
})
names(Matrices) <- unique(x@sample@groups$label)
return(Matrices)
}
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