[R-sig-Geo] Extract Value from Raster Stack Layer Determined by Different Raster's Pixel Value

[Robert J. Hijmans]

Andrew,
I think you can use the stackSelect function for this to shortcut the problem:

# your data
library(raster)
SOST <- raster()
SOST[] <- 1:5
r1 <- r2 <- r3 <- r4 <- r5 <- raster()
r1[] <- 10
r2[] <- 20
r3[] <- 30
r4[] <- 40
r5[] <- 50
GDD <- stack(r1,r2,r3,r4,r5)
#

x <- stackSelect(GDD, SOST)

set.seed(232)
samp <- sampleRandom(SOST, 5, xy = TRUE, na.rm = TRUE)[, -3]
extract(x, samp)

Best, Robert

On Wed, Jul 24, 2013 at 4:02 PM, Andrew Vitale <vitale232 at gmail.com> wrote:
> Hello,
>
> We have a raster which represents the ordinal date corresponding to the
> start of growing season.  That is, each pixel value in the raster lies
> between 1:365, representing the ordinal date.
>
> I have also calculated cumulative growing degree days for all 365 days in
> the corresponding year.  These data are loaded into R as a raster stack
> with 365 layers.
>
> My goal is to randomly sample geographic locations on the start of growing
> season layer.  I then hope to extract the value of cumulative growing
> degree days from those same coordinates, but only from the growing degree
> days stack's layer which corresponds to the start of season pixel value.
>
> For example, if the start of season at a given pixel was the 100th day of
> the year, I would like to extract the growing degree days from that
> location on the 100th day of the year (nlayers = 100).
>
> I have been attempting to write a function to accomplish this, but I can't
> seem to get it to work right.  I would like to end up with a data frame or
> matrix showing my x location, y location, start of season day, and GDD for
> that day.  Instead of many GDD values in one column, I get many columns of
> one GDD value.
>
> It seems the problem is in my use of extract.  I've experimented with the
> arguments nl, layer, and indexing the x argument with [[]].  They seem to
> produce the same result.  Here's a simplified code with only 5 days to
> consider, and the function I am trying to construct.
>
> Any help/suggestions is appreciated!
> Andrew
>
> #============================================================
> library(raster)
>
> SOST <- raster()
> SOST[] <- 1:5
>
> r1 <- r2 <- r3 <- r4 <- r5 <- raster()
> r1[] <- 10
> r2[] <- 20
> r3[] <- 30
> r4[] <- 40
> r5[] <- 50
> GDD <- stack(r1,r2,r3,r4,r5)
>
> getGDD <- function(sost, gdd, n){set.seed(232)
>             samp <- sampleRandom(sost, n, xy = TRUE,
>             na.rm = TRUE)
>
>             df <- data.frame('x'=as.numeric(), 'y'=
>             as.numeric(), 'SOST'=as.numeric(),
>             'GDD'=as.numeric())
>
>
>             df.temp <- data.frame('x' = samp[1:n,1], 'y' =
>             samp[1:n,2], 'SOST' = samp[,3],'GDD' =
>             extract(gdd, samp[1:n,1:2], nl = samp[1:n,3]))
>
>             df <- rbind(df, df.temp)
>             return(df)
>                                         }
>
> getGDD(sost = SOST, gdd = GDD, n = 5)
>
>
>
> --
> *Andrew P. Vitale*
> Masters Student
> Department of Geography
> University of Nevada, Reno
> (412) 915-3632
> vitale232 at gmail.com
>
>         [[alternative HTML version deleted]]
>
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