Dear List, I am having trouble creating a brick out of a raster stack with 9 grids of 2.5 mb each. My goal in creating the brick is to hopefully speed up calculation of quantiles for each grid location, which runs very slowly as follows:
q.10 <- calc(stack1, function(x) quantile(x, 0.1)) I was hoping this would be faster (and I will appreciate any advice on speeding this up) q.10 <- calc(brick1, function(x) quantile(x, 0.1)) But I can't get to it, and I am not sure why. For instance, I have no problem bricking these dummy rasters, which are a bit bigger than my own data. library(raster) library(rgdal) r.list <- lapply(1:9, function(x) { r <- raster(nrow = 800, ncol = 800) r[] <- rnorm(ncell(r)) r <- writeRaster(r, filename = paste("test", x, ".tif", sep = ""), overwrite = T) # Using geotiffs return(r) }) r.stack <- stack(lapply(1:9, function(x) r.list[[x]])) r.brick <- brick(r.stack) # Works fine, takes about 30 seconds - 1 minute # However, when I try the same basic thing with my own rasters, # my system goes into a hang with and R seems to chew up all # remaining memory (~2.5 GB). # Here's an example using one of my rasters link <- "http://www.princeton.edu/~lestes/mri.A2.yld.a.r.tif" download.file(url = link, destfile = "r.tif", method = "wget") r2 <- raster("r.tif") r.list2 <- c(r2, lapply(1:8, function(x) { rst <- writeRaster(r2, filename = paste("r.", x + 1, ".tif", sep = "")) })) # Duplicate the raster 8 times and make a list out of 9 r2.s <- stack(lapply(1:9, function(x) r.list2[[x]])) # Stack them r2.brick <- brick(r2.s) # This hangs the system I am not sure why this is happening, but maybe it has to do with the file itself (assuming I am not coding something incorrectly). Might it have to do with the NA values in it? I will appreciate any pointers on fixing this and on the quantile calculation method. Thanks in advance. My sessionInfo follows the signoff. Cheers, Lyndon R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] raster_1.9-33 doBy_4.4.2 MASS_7.3-16 snow_0.3-7 lme4_0.999375-42 Matrix_1.0-1 lattice_0.20-0 multcomp_1.2-8 [9] mvtnorm_0.9-9991 R2HTML_2.2 survival_2.36-10 rgdal_0.7-1 sp_0.9-91 loaded via a namespace (and not attached): [1] grid_2.14.0 nlme_3.1-102 stats4_2.14.0 tools_2.14.0 _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo