Copy multiple raster filenames in a single CSV file in R

Question

Can somebody help me on how to copy multiple filenames in a single CSV file? I have 365 raster files and a polygon dataset with 5 features. What I am trying to do is extract cell values corresponding to polygon features. I am able to do this but not able to copy the corresponding raster filenames in a single CSV. Below is my code:

library(rgdal)
library(raster)

setwd("C:/PHP_Win7/Etios/2007")
polygong <- readOGR("C:/PHP_Win7/Etios/2007", "Ethn")
rasterfiles <- list.files(".", pattern = "tif")

for (j in 1:length(rasterfiles)) {
  curRaster <- raster(paste("C:/PHP_Win7/Etios/2007", rasterfiles[j], sep = "/"))
  csvDatatoWrite <- data.frame(coordinates(polygong),
                               polygong$Name,
                               extract(curRaster, polygong))
  write.table(csvDatatoWrite, file = "output.csv",
              append = TRUE, sep = ",", row.names = F)
}

The output I am getting is

I would like to replace "extract.curRaster..polygong." column heading in output sample with corresponding filenames. Any help on this?

Answer 1

Your assumed data structure is not correct. Given a polygon feature class, using the extract function will result in a list object with multiple raster cell values associated with each polygon. The way you are collapsing the data in a data.frame will yield unexpected and undesirable results.

You need to create an object using extract and the use lapply to summarize the raster data (eg., mean of raster) for each polygon. This will result in a vector that can then be directly matched to your polygon object.

This is readily illustrated in this modified example of extract's documentation.

library(raster)
r <- raster(ncol=50, nrow=50)
  r[] <- runif(ncell(r))
polys <- spPolygons(rbind(c(-180,-20), c(-160,5), c(-60, 0), c(-160,-60), c(-180,-20)),
                    rbind(c(80,0), c(100,60), c(120,0), c(120,-55), c(80,0)))
    polys <- SpatialPolygonsDataFrame(polys, data.frame(ID=1:2))

plot(r)
plot(polys, add=TRUE)

# Extract raster values for each polygon and check object class
( v <- extract(r, polys) )
class( v )

# Use lapply to summarize polygon raster values to mean
( v <- unlist(lapply( v, mean)) )
class( v )

# Join raster means to @data slot in polys
polys@data["r"] <- unlist(lapply( v, mean))
  polys@data["r"]

# Write csv of polygon attributes
write.csv( polys@data, "myfile.csv", row.names = FALSE)

If you, in fact, want all of the raw values associated with each polygon it will be very difficult to write this into a single csv containing all of the polygons, rasters and unique values (which will vary by polygon). You will really need to rethink your data structure and associated code.