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.davenp...@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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo