From: Ray Brownrigg <Ray.Brownrigg_at_mcs.vuw.ac.nz>

Date: Mon, 07 Jul 2008 08:26:41 +1200

R-help_at_r-project.org mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sun 06 Jul 2008 - 20:32:23 GMT

Date: Mon, 07 Jul 2008 08:26:41 +1200

You are doing a lot of unnecessary work inside each loop. For example the function regression() is defined as many as rows*cols times, but only needs to be defined once. Similarly getgrid() and getslice() (which does need to be defined inside the j loop, but not inside the k loop).

**HTH
**

Ray Brownrigg

On Mon, 07 Jul 2008, Zarza wrote:

> Hello,

*> we have 80 text files with matrices. Each matrix represents a map (rows for
**> latitude and columns for longitude), the 80 maps represent steps in time.
**> In addition, we have a vector x of length 80. We would like to compute a
**> regression between matrices (response through time) and x and create maps
**> representing coefficients, r2 etc. Problem: the 80 matrices are of the size
**> 4000 x 3500 and we were running out of memory. We computed line by line and
**> the results for each line were appended to output grids. This works. But -
**> for each line, 80 text files must be scanned and output must be written.
**> And there are several for-loops involved. This takes a lot of time (about a
**> week). I read the contributions related to speeding up code and maybe
**> vectorizing parts of the procedure could help a bit. However, I am a
**> neophyte (as you may see from the code below) and did not find a way by
**> now. I would appreciate very much any suggestions for speeding up the
**> procedure. Thanks, Zarza
**>
**>
**>
**>
**> The code (running but sloooooow):
**> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
**> regrid <- function (infolder, x, outfolder) {
**>
**> # List of input files
**> setwd (infolder)
**> filelist <- dir (pattern=".*.asc$", full.names = F)
**>
**> # Dimensions (making use of the header information coming with
**> # the .asc-input files, ESRI-format)
**> hd <- read.table (filelist [1], nrows = 6)
**> cols <- hd[1,2]
**> rows <- hd[2,2]
**> times <- length (filelist)
**> items <- 4 + ncol (x)
**>
**> # Prepare output
**> out1 <- matrix (numeric (times * cols), ncol = cols)
**> out2 <- matrix (numeric (items * cols), ncol = items)
**> out3 <- as.numeric (items)
**>
**> # Prepare .asc-files
**> filenames <- c("R2", "adj.R2", "p", "b0", colnames (x))
**> for (i in 1:items) {
**> write.table (hd, file = paste (outfolder, filenames [i],".asc",sep =""),
**> quote=F, row.names=F, col.names=F) }
**> rm (hd)
**>
**> # Prepare regression
**> xnam <- paste ("x[,", 1:(ncol(x)),"]", sep="")
**> form <- paste("y ~ ", paste(xnam, collapse="+"))
**> rm (xnam)
**>
**> # Loop through rows
**> for (j in 1:rows) {
**> getgrid <- function (j) {
**> print (paste ("Row",j,"/",rows),quote = F)
**>
**> # Read out multi-temporal response values for one grid-row of cells
**> for (k in 1:times)
**> {
**> getslice <- function (k) {
**> values <- scan (filelist [k], what=0, na.strings = "-9999",
**> skip = (5 + j), nlines = 1, nmax = cols, quiet=T)
**> values }
**> out1[k,] <- getslice (k)
**> }
**>
**> # Regression
**> for (l in 1:cols)
**> {
**> y <- as.vector (out1 [,l])
**> if (length (y) > length (na.omit (y)))
**> {
**> setNA <- function (l) {
**> NAs <- rep (NA, length (out3))
**> NAs }
**> out2[l,] <- setNA (l)
**> }
**> else
**> {
**> regression <- function (l) {
**> model <- lm (as.formula(form))
**> out3[1] <- summary (model)$r.squared
**> out3[2] <- summary (model)$adj.r.squared
**> f <- summary (model)$fstatistic
**> out3[3] <- 1-pf(f[1],f[2],f[3])
**> out3[4:items] <- coef(model)[1:(1 + ncol(x))]
**> out3 }
**> out2[l,] <- regression (l)
**> }
**> }
**> out2
**> }
**> fillrow <- getgrid (j)
**>
**> # Append results to output files
**> for (m in 1:items) {
**> write.table (t(fillrow [,m]), file = paste (outfolder, filenames [m],
**> ".asc", sep =""), append=T, quote=F, na = as.character (-9999),
**> row.names = F, col.names = F, dec=".") }
**> }
**> }
*

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sun 06 Jul 2008 - 20:32:23 GMT

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