Oddly enough, the variogram modelling is rather quick in Surfer, but one cannot compute the standard errors. I restricted the search to the approximate the range of the variogram model (2000m). I can get R to compute with 12079 observations, but 13453 and I run into the gstat error message.
I guess it's really down to 1) trying to reduce the original dataset 2) adding 1 to 2 Gb of RAM 3) running the predictions on a Linux machine with suitable RAM. I couldn't reproduce the memory.limit() issue. I'll chalk that up to errant typing on my part. Quoting Rubén Roa-Ureta <[EMAIL PROTECTED]>: > I think any geostatistical program/R package would have trouble > handling 12000 observations on a PC. The empirical variogram would be > built with the combinations of 12000 over 2 pairs, nearly 72 millions > pairs, and during kriging, if you didn't restrict the search > neighbourhood, interpolation would involve solving something very big, > more so if you defined a fine grid, ... Try restricting the search > neighbourhood, if you didn't, with maxdist and nmax. > > Rubén > > > Prof Brian Ripley wrote: >> I think the clue is that the message you quote comes from gstat, >> which does not use R's memory allocator. It is gstat and not R >> that has failed to allocate memory. >> >> Try re-reading the help page for memory.size. 'max=T' does not >> indicate the limit (that is the job of memory.limit()), but the >> maximum 'used' (acquired from the OS) in that session. So 19Mb >> looks reasonable for R's usage. >> >> I don't understand the message from memory.limit() (and the >> formatting is odd). memory.limit() does not call max() (it is >> entirely internal), so I wonder if that really is the output from >> that command. (If you can reproduce it, please let us have precise >> reproduction instructions.) >> >> There isn't much point in increasing the memory limit from the >> default 1.5Gb on a 2Gb XP machine. The problem is that the user >> address space limit is 2Gb and fragmentation means that you are >> unlikely to be able to get over 1.5Gb unless you have very many >> small objects, in which case R will run very slowly. In any case, >> that is not the issue here. >> >> On Wed, 16 Apr 2008, Dave Depew wrote: >> >>> Hi all, >>> I've read the R for windows FAQ and am a little confused re: >>> memory.limit and memory.size >>> >>> to start using R 2.6.2 on WinXP, 2GB RAM, I have the command line "sdi >>> --max-mem-size=2047M" >>> Once the Rgui is open, memory.limit() returns 2047, memory.size() >>> returns 11.315, and memory.size(max=T) returns 19.615 >>> >>> Shouldn't memory.size(max=T) return 2047? >>> >>> Upon running several operations involving kriging (gstat package, >>> original data file 3 variables, 12000 observations) >>> the program runs out of memory >>> >>> "memory.c", line 57: can't allocate memory in function m_get() >>> Error in predict.gstat(fit.uk, newdata = EcoSAV.grid.clip.spxdf, >>> debug.level = -2, : >>> m_get >>> >>> Immediately following this, >>> >>> memory.limit() returns [1] -Inf >>> Warning message: >>> In memory.limit() : no non-missing arguments >>> to max; returning -Inf >>> >>> memory.size() returns 24.573. >>> >>> memory.size(max=T) returns 46.75 >>> >>> To my untrained eye, it appears that R is not being allowed access to >>> the full memory limit specified in the cmd line....if this is the case, >>> how does one ensure that R is getting access to the full allotment of RAM? >>> Any insight is appreciated... >>> >>> >>>> sessionInfo() >>> R version 2.6.2 (2008-02-08) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets tcltk utils >>> methods base >>> >>> other attached packages: >>> [1] maptools_0.7-7 foreign_0.8-23 gstat_0.9-43 rgdal_0.5-24 >>> lattice_0.17-4 sp_0.9-23 svSocket_0.9-5 svIO_0.9-5 >>> R2HTML_1.58 svMisc_0.9-5 svIDE_0.9-5 >>> >>> loaded via a namespace (and not attached): >>> [1] grid_2.6.2 tools_2.6.2 >>> >>> ______________________________________________ >>> R-help@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. >>> >> ______________________________________________ R-help@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.
