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### precompute.R ---
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## Author: Brice Ozenne
## Created: sep 22 2021 (13:47)
## Version:
## Last-Updated: okt 5 2022 (11:40)
## By: Brice Ozenne
## Update #: 27
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### Commentary:
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### Change Log:
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### Code:
## * .precomputeXX
## Precompute square of the design matrix
.precomputeXX <- function(X, pattern, pattern.ntime, pattern.cluster, index.cluster){
p <- NCOL(X)
n.pattern <- length(pattern)
out <- list(pattern = stats::setNames(lapply(pattern, function(iPattern){matrix(0, nrow = pattern.ntime[iPattern]*pattern.ntime[iPattern], ncol = p*(p+1)/2)}), pattern),
key = matrix(as.numeric(NA),nrow=p,ncol=p,dimnames=list(colnames(X),colnames(X))),
Xpattern = stats::setNames(vector(mode = "list", length = n.pattern),pattern))
## key
out$key[lower.tri(out$key,diag = TRUE)] <- 1:sum(lower.tri(out$key,diag = TRUE))
out$key[upper.tri(out$key)] <- t(out$key)[upper.tri(out$key)]
## fill matrix
for(iPattern in pattern){ ## iPattern <- pattern[1]
iTime <- pattern.ntime[iPattern]
if(iTime==1){
out$Xpattern[[iPattern]] <- do.call(rbind,lapply(index.cluster[pattern.cluster[[iPattern]]], function(iIndex){X[iIndex,,drop=FALSE]}))
iX.summary <- crossprod(out$Xpattern[[iPattern]])
## out$key[lower.tri(out$key,diag = TRUE)]
out$pattern[[iPattern]][1,] <- iX.summary[lower.tri(iX.summary, diag = TRUE)]
}else{
out$Xpattern[[iPattern]] <- array(unlist(lapply(index.cluster[pattern.cluster[[iPattern]]], function(iIndex){X[iIndex,,drop=FALSE]})),
dim = c(iTime,NCOL(X),length(index.cluster[pattern.cluster[[iPattern]]])),
dimnames = list(NULL,colnames(X),NULL))
for(iCol1 in 1:p){ ## iCol1 <- 1
for(iCol2 in 1:iCol1){ ## iCol2 <- 2
## for(iId in pattern.cluster[[iPattern]]){
## out$pattern[[iPattern]][,,out$key[iCol1,iCol2]] <- out$pattern[[iPattern]][,,out$key[iCol1,iCol2]] + tcrossprod(X[index.cluster[[iId]],iCol1,drop=FALSE],X[index.cluster[[iId]],iCol2,drop=FALSE])
## }
out$pattern[[iPattern]][,out$key[iCol1,iCol2]] <- tcrossprod(out$Xpattern[[iPattern]][,iCol1,],out$Xpattern[[iPattern]][,iCol2,])
}
}
}
}
return(out)
}
## * .precomputeXR
## Precompute design matrix times residuals
.precomputeXR <- function(X, residuals, pattern, pattern.ntime, pattern.cluster, index.cluster){
p <- NCOL(X[[1]])
name.mucoef <- colnames(X[[1]])
n.pattern <- length(pattern)
out <- stats::setNames(lapply(pattern, function(iPattern){
array(0, dim = c(pattern.ntime[iPattern], pattern.ntime[iPattern], ncol = p), dimnames = list(NULL,NULL,name.mucoef))
}), pattern)
for(iPattern in pattern){ ## iPattern <- pattern[1]
iTime <- pattern.ntime[iPattern]
iResiduals <- do.call(cbind, lapply(index.cluster[pattern.cluster[[iPattern]]], function(iIndex){residuals[iIndex,,drop=FALSE]}))
iX <- X[[iPattern]]
if(iTime == 1){
out[[iPattern]][1,1,] <- iResiduals %*% iX
}else{
for(iCol in 1:p){ ## iCol1 <- 1
## for(iId in 1:length(pattern.cluster[[iPattern]])){ ## iId <- 1
## out[[iPattern]][,,iCol] <- out[[iPattern]][,,iCol] + tcrossprod(iX[[iId]][,iCol,drop=FALSE],iResiduals[[iId]])
## }
out[[iPattern]][,,iCol] <- tcrossprod(iX[,iCol,], iResiduals)
}
}
}
return(out)
}
## * .precomputeRR
## Precompute square of the residuals
.precomputeRR <- function(residuals, pattern.ntime, pattern, pattern.cluster, index.cluster){
n.pattern <- length(pattern)
out <- stats::setNames(lapply(pattern, function(iPattern){
matrix(0, nrow = pattern.ntime[iPattern], ncol = pattern.ntime[iPattern])
}), pattern)
for(iPattern in pattern){ ## iPattern <- pattern[1]
## for(iId in pattern.cluster[[iPattern]]){
## out[[iPattern]] <- out[[iPattern]] + tcrossprod(residuals[index.cluster[[iId]],,drop=FALSE])
## }
out[[iPattern]] <- tcrossprod(do.call(cbind,lapply(index.cluster[pattern.cluster[[iPattern]]], function(iIndex){residuals[iIndex,,drop=FALSE]})))
}
return(out)
}
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### precompute.R ends here
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