lapply to convert rasters to polygons using gdal_polygonizeR - polygon

Question

I am using John Baumgrtner's gdal_polygonizeR (https://johnbaumgartner.wordpress.com/2012/07/26/getting-rasters-into-shape-from-r/) to covert rasters to polygons in R. Aside - I tried raster pkg rasterToPolygons function and it took forever; gdal_polygonizeR is way faster. Anyways, I have a list of 533 raster files (different extents) that I want to convert to polygons. The gdal_polygonizeR function works when a single list element is called, but I have tried to use it on all list elements using lapply and get an error message. See code below:
#path to folder containing all .tif raster files
dir <- "/path/to/raster/files"
#create a list of the files in the folder
files <- list.files(path = dir, pattern = ".tif$")
#use lapply to import/create list of all files in folder
rasterl_50 <- lapply(paste0(dir, files), raster)
#test gdal_polygonizeR function on single list element
gdal_polygonizeR(rasterl_50[[1]]) #works properly
#loop thru all elements in list
lapply(rasterl_50, gdal_polygonizeR)
Output = the first six (6) elements seem to run OK, but I get the following error msg at [[7]]:
wfp1 <- gdal_polygonizeR(rasterl_50[[1]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d4dc99d8d.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp2 <- gdal_polygonizeR(rasterl_50[[2]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d7698a853.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp3 <- gdal_polygonizeR(rasterl_50[[3]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d30d4d703.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp4 <- gdal_polygonizeR(rasterl_50[[4]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d24036d07.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp5 <- gdal_polygonizeR(rasterl_50[[5]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d4683ed87.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp6 <- gdal_polygonizeR(rasterl_50[[6]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d4e23b4d1.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
wfp7 <- gdal_polygonizeR(rasterl_50[[7]])
Creating output /var/folders/s9/pm92gdl94h18k4n6026cb8x00000gn/T//RtmpvRRvA4/file23d6791d108.shp of format ESRI Shapefile.
0...10...20...30...40...50...60...70...80...90...100 - done.
Error in readOGR(dirname(outshape), layer = basename(outshape), verbose = !quiet) :
no features found
In addition: Warning message:
In ogrFIDs(dsn = dsn, layer = layer) :
Show Traceback
Rerun with Debug
Error in readOGR(dirname(outshape), layer = basename(outshape), verbose = !quiet) :
no features found
#
If anyone has ideas for a solution using lapply or a for loop etc., please reply. Thanks

Answer 1

Solution: I had to run gdal_polygonizeR on each individual list element, and found that several raster files in the list contained no values (this resulted from reclassify function applied to rasters prior). I removed these files from the list, and lapply worked. Here is the code:
#remove 'no value' elements from the list
new_rastlist <-
rasterlist[c(-7,-14,-36,-89,-191,-310,-432,-436,-476,-493,-494,-501)]
#then try again to use lapply
polyl <- lapply(rastlist, gdal_polygonizeR)
UPDATE:
Even better, remove rasters with all NAs first with this:
batch_reclass <- function(rastlist){
for (i in 1:length(wfrastlist)) {
#read in raster
r <-raster(paste0("/path/to/rasterfiles/", rastlist[i]))
#perform the reclassifcation
rc <- reclassify(r, rclmat)
#write each reclass to a new file
if (!is.na(minValue(rc))) {
writeRaster(rc, filename = paste0("/path/to/new/rasterfiles/", "rc_",
rastlist[i]), format="GTiff", overwrite=TRUE)
}}
}
#run the function
batch_reclass(rastlist)