[R-sig-Geo] SGDF loop processing time

[Roger Bivand]

On Wed, 25 Jun 2008, Ilona Naujokaitis-Lewis wrote:

>
>
> Dear List-serve,
>
> I have written a loop that creates a Spatial Grid Dataframe from 2 other
> SGDFs. I am interested in finding out if there is a way to decrease the
> processing time of the entire loop. I am aware that loops in R are not the
> most efficient way to go, but based on my knowledge, I am not sure how to
> get around this. To avoid problems with memory allocation I have added gc()
> command throughout the loop.
>
> The system.time() results for the loop (see code below) with a small (16x12)
> grid is:
> user  system elapsed
> 17.08    0.02   17.22
>
> The problem is when I work with larger grids (i.e. greater than dimensions:
> 900x1200). The processing time is in the order of 24 hours.
>
> I have checked threads for help on both decreasing the memory size, and
> writing efficient code. Any suggestions on how I might decrease the
> processing time, as this is the biggest concern right now (both using and
> not using R, but the former preferred), would be greatly appreciated.
>
> Here is the code with a brief description of the objects.
>
>
> Objects:
> prePatchmap: SGDF, binary (0,1)
> mean_HS: mean habitat suitability value of original habitat suitability map
> sd_HS: standard deviation of original habitat suitability map
> new_HSthreshold: new habitat suitability threshold
> HSthreshold: original habitat suitability threshold
> HSmap: SGDF of original habitat suitability values

Could you provide an online example - save() the objects you need here and 
post the RData file? This does look vectorisable, at least in two chunks.

Roger

>
> for (i in 1:length(prePatchmap$patch))
>    {
>    if (prePatchmap$patch[i]==1)
>       {
>       prePatchmap$NPHS[i]<-round(rnorm(1, mean_HS, sd_HS),digits=3)
>       gc()
>          {
>          if (prePatchmap$NPHS[i]<new_HSthreshold)
>            {
>            prePatchmap$NPHS[i]<-new_HSthreshold
>            gc()
>            }
>          }
>       } else
>       {
>       if (HSmap$HSvalue[i]<HSthreshold)
>            {
>            prePatchmap$NPHS[i]<-HSmap$HSvalue[i]
>            }
>       gc()
>       }
>     }
>
>
> Cheers,
>
> Ilona Naujokaitis-Lewis
>
>
> Ilona Naujokaitis-Lewis
> Centre for Applied Conservation Research
> Forest Sciences Department
> University of British Columbia
> 3041-2424 Main Mall
> Vancouver, BC V6T 1Z4
>
> phone: 604 822.4382
> email: ilonan at interchange.ubc.ca
>
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>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no