[R] Efficient coding

[Daniele Amberti]

I have a piece of code as the one at the bottom, unfortunately since it involves time series from a db it's not easy to give to mailing list a working script.
It becomes very slow after few hundred iterations over variable sp (must process several thousands).
The Rprof() indicates that the problem is the use of gc(). Can someone indicate what I have to take care of not to call gc() so often?

Thanks in advance


-----
toProcess <- unique(tsr$cSpillingPointID)
first <- 1
for(sp in toProcess)
{
  tsrSUB <- tsr[tsr$cSpillingPointID == sp,]
  dmnd <- tsrSUB[is.na(tsrSUB$cDeviceClass),]
  if(nrow(dmnd) != 1)
    warning(paste("cSpillingPointID", sp, "has more than one demand time Series. Used first."))

  tsrValCount <- getTimeSeries(chn, tsrSUB[!is.na(tsrSUB$cDeviceClass),]$cTimeSeriesID, nDaysBack = 366*nyears)
  tsrValDmnd  <- getTimeSeries(chn, dmnd$cTimeSeriesID[1], nDaysBack = 366*nyears)

  sequence <- timeSequence(from = format(start(tsrValDmnd), '%Y-%m-%d'), to = format(end(tsrValDmnd), '%Y-%m-%d'), by = 'day')
  if(format(start(tsrValDmnd), '%H') != '00')
    tsrValDmnd <- window(tsrValDmnd, sequence[3], end(tsrValDmnd))
  if(format(end(tsrValDmnd), '%H') != '23')
    tsrValDmnd <- window(tsrValDmnd, start(tsrValDmnd), sequence[length(sequence)-2])

  sequence <- sequence - 3600
  tsrValDmnd <- aggregate(tsrValDmnd, by = sequence, sum)
  sequence <- seriesPositions(tsrValDmnd)
  newPositions(tsrValDmnd) <- sequence - 23*3600
  #head(tsrValDmnd2)
  #sum(head(tsrValDmnd, 24))
  tsrValSub <- cbind(tsrValDmnd, tsrValCount)
  tsrValSub <- na.omit(tsrValSub)
  head(tsrValSub)

  if(nrow(tsrValSub) > 1)
  {
  dif <- na.omit(tsrValSub[,-1] -lag(tsrValSub[,-1],1))
  head(dif)

  costant <- is.costant(dif)
  if(any(costant == FALSE))
  {
    a <- (dif != 0) *1:nrow(dif)
    a <- seriesPositions(dif[abs(a[a!=0]),])
    from <- min(a) - ndays *24*60*60
    to <- max(a) + ndays *24*60*60
    tsrValSub <- window(tsrValSub, from, to)
  }  else
  {
    if(nrow(tsrValSub) > ndays) tsrValSub <- sample(tsrValSub, ndays)
  }

  if(nrow(tsrValSub) > 1)
  {
    row.names(tsrSUB) <- tsrSUB$cTimeSeriesID
    if(any(is.na(tsrSUB$cDeviceClass)))
      tsrSUB[is.na(tsrSUB$cDeviceClass),]$cDeviceClass <- 'DMND'

    tsrValSub at units <- tsrSUB[tsrValSub at units,]$cDeviceClass

    if(first == 1)
      dat <- data.frame(cSpillingPointID = sp,
                        year = format(seriesPositions(tsrValSub), '%Y'),
                        month = format(seriesPositions(tsrValSub), '%m'),
                        day = format(seriesPositions(tsrValSub), '%d'),
                        tsrValSub,
                        stringsAsFactors = F)
    else
      dat <- merge(dat,
                   data.frame(cSpillingPointID = sp,
                              year = format(seriesPositions(tsrValSub), '%Y'),
                              month = format(seriesPositions(tsrValSub), '%m'),
                              day = format(seriesPositions(tsrValSub), '%d'),
                              tsrValSub,
                              stringsAsFactors = F),
                   all.x = T, all.y = T)

    cat(paste('Added', nrow(tsrValSub), 'rows.\n'))
    cat(paste('...', round(first/length(toProcess)*100, 2), '%...\n'))
  }
  }
  else cat(paste('...', round(first/length(toProcess)*100, 2), '%...\n'))

  if(any(first %in% seq(100, length(toProcess), 250) )) gc()
  first <- first +1
}
----

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