[R-sig-Geo] raster Median function very slow on stack compared to mean: expected behavior?

[Robert Hijmans]

> I am trying to extract the per-pixel median from a raster stack, and 
> am finding that the process takes a very long time relative to taking 
> the per-pixel mean. It is long enough that I have never actually seen 
> whether it successfully completes on my data, but this dummy example 
> shows the code structure I am using and the time differences between 
> the two functions: 
> 
> stk <- stack(lapply(1:10, function(x) { 
>  r <- raster(nrow = 1000, ncol = 1000) 
>  r2 <- setValues(r, sample(1:100, size = ncell(r), replace = T, prob =
> NULL)) 
> })) 
>
> setOptions(todisk = TRUE)  # I used this option to rule out memory issues 
> t1 <- Sys.time() 
> med <- calc(stk, Median, filename = "med.tif", datatype = "INT2S", 
> overwrite = T) 
> Sys.time() - t1  # 7.26 mins 
>
> t2 <- Sys.time() 
> med <- calc(stk, mean, filename = "mean.tif", datatype = "INT2S",
> overwrite = T) 
> Sys.time() - t2  # 2.34 secs 
> setOptions(todisk = FALSE) 
> 
>
> Am I doing something wrong with my code, or is the speed difference I 
> am seeing expected? 
>

Lyndon, 

Median (big M) was intended for use like Median(s) not for use in calc
(which did not exist yet); but I am surprised how slow it is in calc. Now we
have calc, you can use median (small m) and that is much quicker; and about
the same as Median(s); I think I will remove Median as it is no longer
needed. 

Either way, median will be slower than mean, which is expected:

> v = runif(1e+7)
> system.time(mean(v))
   user  system elapsed 
   0.09    0.00    0.09 
> system.time(median(v))  # 7 times slower
   user  system elapsed 
   0.56    0.06    0.63 
> 
> s <- stack(sapply(1:10, function(x) setValues(r, runif(ncell(r)))))
> r <- raster()
> 
> system.time(mean(s))
   user  system elapsed 
   4.75    0.02    4.79 
> system.time(calc(s, mean))
   user  system elapsed 
   0.25    0.00    0.26 

> system.time(Median(s))
   user  system elapsed 
   7.73    0.00    7.75 
> system.time(calc(s, median))
   user  system elapsed 
   8.48    0.00    8.54 
> system.time(calc(s, Median)) # slow!
   user  system elapsed 
  28.15    0.03   28.27 
> 
> 


Robert




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