[R-sig-Geo] raster::extract fails on brick but works on individual layers of brick
Lyndon Estes
lyndon.estes at gmail.com
Wed Jul 23 19:07:42 CEST 2014
Hi Frank,
I think the mean function is getting in the way, since if you want to
extra the values for all cells each polygon overlaps, the outputs will
first end up in a list.
test1 <- extract(g, dsd, weights = TRUE, small = TRUE)
Will get the cell values for each polygon from each layer in the
brick, along with their weight (while allowing very small polygons to
get their underlying cell values).
I would then process the mean function on the list.
v <- t(sapply(test1, function(x) apply(t(sapply(1:nrow(x), function(y)
x[y, 1:10] * x[y, 11])), 2, sum))) # matrix of annual values per
polygon
Hope this helps.
Cheers, Lyndon
On Wed, Jul 23, 2014 at 12:17 PM, Frank Davenport
<frank.davenport at gmail.com> wrote:
> Hello,
>
> I am using extract() to aggregate values from a raster to a polygon. The
> raster is a brick object. Extract fails on the brick object but succeeds
> when applied on each individual layer of the brick (via a for() loop). I
> would use this as a work around but in my actual scenario the brick is much
> bigger and the individual approach is too slow.
>
> The specific error message is: "Error in t(sapply(res, meanfunc)) : error
> in evaluating the argument 'x' in selecting a method for function 't':
> Error in apply(x, 1, function(X) { : dim(X) must have a positive length"
>
> I believe this has something to do with the relative sizes of the polygons
> (small) and the grid cells. I have successfully extracted this brick to
> another shapefile that had much larger polygons. Likewise I can also do the
> extraction if I resample the cells to a smaller resolution (not shown
> below).
>
>
> Finally the extract will work if I set 'na.rm=F' but then produces mostly
> NA's, even though there are no NAs in the brick. I realize this might be
> something to do with the dataType(). However that does not explain why
> extract works on individual layers, but not the whole brick.
>
> Reproducible code is below and prettier example can be found here:
> http://rpubs.com/frank_davenport/22698
>
> The data necessary to run the example can be found here:
> https://dl.dropboxusercontent.com/u/9577903/99_raster_bugreport.Rdata
>
> Thank you for your help and apologies if a solution is already posted.
>
> Frank
>
>> rm(list=ls())
>> library(raster)
> Loading required package: sp
>>
>> ##-Download data from here:
> https://dl.dropboxusercontent.com/u/9577903/99_raster_bugreport.Rdata
>>
>> ##contains 'dsd' a spatial polygons data.frame and 'g' a raster brick
> with 10 layers
>> load('~/Dropbox/Public/99_raster_bugreport.Rdata')
>>
>> dsd
> class : SpatialPolygonsDataFrame
> features : 36
> extent : 34.04665, 39.70319, -4.67742, 1.19921 (xmin, xmax, ymin,
> ymax)
> coord. ref. : +proj=longlat +a=6378249.145 +b=6356514.96582849 +no_defs
> variables : 4
> names : Province, District, Division, uidu
> min values : CENTRAL, BUNGOMA, ABOTHUGUCHI WEST, 1
> max values : WESTERN, VIHIGA, WINAM, 44
>> g
> class : RasterBrick
> dimensions : 24, 20, 480, 10 (nrow, ncol, ncell, nlayers)
> resolution : 0.5, 0.5 (x, y)
> extent : 33, 43, -6, 6 (xmin, xmax, ymin, ymax)
> coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> data source : in memory
> names : X1999.03.01, X1999.03.02, X1999.03.03, X1999.03.04,
> X1999.03.05, X1999.03.06, X1999.03.07, X1999.03.08, X1999.03.09,
> X1999.03.10
> min values : 22.47562, 22.44415, 22.25507, 22.23166,
> 22.12387, 22.42477, 22.27802, 22.15134, 22.36218, 22.33447
> max values : 41.47818, 40.53116, 41.54944, 42.33093,
> 41.67810, 40.79260, 41.83319, 40.83359, 41.12604, 42.00555
>
>>
>> #---Show the data
>> plot(g[[1]])
>> plot(dsd,add=T)
>>
>> #--Try to extract, with weights yeilds an error
>> test1<-extract(g,dsd,fun=mean,na.rm=T,weights=T)
> Error in t(sapply(res, meanfunc)) :
> error in evaluating the argument 'x' in selecting a method for function
> 't': Error in apply(x, 1, function(X) { : dim(X) must have a positive length
>>
>> #--Extract without weights--produces NA's for most polygons
>> test2<-extract(g,dsd,fun=mean,na.m=T)
>> head(test2)
> X1999.03.01 X1999.03.02 X1999.03.03 X1999.03.04 X1999.03.05
> X1999.03.06 X1999.03.07 X1999.03.08 X1999.03.09 X1999.03.10
> [1,] NA NA NA NA NA
> NA NA NA NA NA
> [2,] NA NA NA NA NA
> NA NA NA NA NA
> [3,] NA NA NA NA NA
> NA NA NA NA NA
> [4,] NA NA NA NA NA
> NA NA NA NA NA
> [5,] NA NA NA NA NA
> NA NA NA NA NA
> [6,] NA NA NA NA NA
> NA NA NA NA NA
>> summary(test2)
> X1999.03.01 X1999.03.02 X1999.03.03 X1999.03.04
> X1999.03.05 X1999.03.06 X1999.03.07 X1999.03.08
> Min. :24.47 Min. :25.21 Min. :24.67 Min. :25.47 Min.
> :27.42 Min. :25.38 Min. :25.93 Min. :24.11
> 1st Qu.:29.29 1st Qu.:30.99 1st Qu.:29.55 1st Qu.:30.83 1st
> Qu.:31.58 1st Qu.:29.78 1st Qu.:29.51 1st Qu.:28.35
> Median :30.31 Median :33.63 Median :31.13 Median :31.88 Median
> :33.32 Median :30.31 Median :30.52 Median :29.71
> Mean :29.87 Mean :32.75 Mean :30.41 Mean :31.78 Mean
> :32.61 Mean :29.71 Mean :29.90 Mean :29.19
> 3rd Qu.:31.86 3rd Qu.:36.08 3rd Qu.:32.59 3rd Qu.:34.37 3rd
> Qu.:34.73 3rd Qu.:30.60 3rd Qu.:31.32 3rd Qu.:30.82
> Max. :32.81 Max. :37.00 Max. :33.45 Max. :35.77 Max.
> :35.42 Max. :31.98 Max. :31.69 Max. :32.53
> NA's :30 NA's :30 NA's :30 NA's :30 NA's
> :30 NA's :30 NA's :30 NA's :30
> X1999.03.09 X1999.03.10
> Min. :25.98 Min. :25.53
> 1st Qu.:29.53 1st Qu.:30.73
> Median :30.57 Median :31.06
> Mean :30.12 Mean :31.24
> 3rd Qu.:31.41 3rd Qu.:33.52
> Max. :32.75 Max. :34.83
> NA's :30 NA's :30
>>
>> #--Extract each layer seperatley--works but is SLOW
>> glist<-vector(mode='list',length=nlayers(g))
>>
>> for(i in 1:length(glist)){
> + glist[[i]]<-extract(g[[i]],dsd,fun=mean,na.rm=T,weigths=T)
> + }
>>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] raster_2.2-31 sp_1.0-15
>
> loaded via a namespace (and not attached):
> [1] grid_3.1.0 lattice_0.20-29 tools_3.1.0
>>
>
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