[R-sig-Geo] summing rasters with a condition given by other rasters

[Ben Tupper]

Hi Martin,

On May 18, 2015, at 12:22 PM, Martin Brandt <martin.brandt at mailbox.org> wrote:

> Hi Eder,
> 
> yes, i tried to include na.rm:
> 
> sum_segment <- function(x, ...) {
> mean(x[(x[1]+2):(x[2] + 2)], na.rm=TRUE)
> } 
> 
> but as long my stack contains any NA values, the function will not run with
> calc:
>> s <- calc(b, sum_segment)
> Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) : 
>  cannot use this function
> 
> or
> 
>> s <- calc(b, sum_segment, na.rm=T)
> Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) : 
>  cannot use this function. Perhaps add '...' or 'na.rm' to the function
> arguments?
> 
> not sure how to make the function run and ignore all NAs..
> 

This function is designed to accept further arguments for other functions within the its body.  So, if you pass na.rm = TRUE to sum_segment() then it will trickle down, so to speak, to sum().  The following should work for sum or mean.

sum_segment <- function(x, ...) {
  sum(x[(x[1]+2):(x[2] + 2)],...)
}

mean_segment <- function(x, ...) {
  mean(x[(x[1]+2):(x[2] + 2)],...)
}


s <- calc(b, sum_segment, na.rm = TRUE)
m <- calc(b, mean_segment, na.rm = TRUE)

s
#class       : RasterLayer 
# dimensions  : 77, 101, 7777  (nrow, ncol, ncell)
# resolution  : 1, 1  (x, y)
# extent      : 0, 101, 0, 77  (xmin, xmax, ymin, ymax)
# coord. ref. : +proj=merc 
# data source : in memory
# names       : layer 
# values      : 0, 2295  (min, max)

m
# class       : RasterLayer 
# dimensions  : 77, 101, 7777  (nrow, ncol, ncell)
# resolution  : 1, 1  (x, y)
# extent      : 0, 101, 0, 77  (xmin, xmax, ymin, ymax)
# coord. ref. : +proj=merc 
# data source : in memory
# names       : layer 
# values      : 0, 255  (min, max)



If that doesn't work (whether you use mean() or sum()) then something else is happening and you'll want to post a small runnable example of what you are doing.   
 
Cheers,
Ben

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Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org