Clipping raster using shapefile in R, but keeping the geometry of the shapefile

23
votes

I am using {raster} to clip (or crop) a raster based on an irregular shapefile (the Amazon biome) but the output always has a rectangular extent. However, I need the output in the exact same geometry of the shapefile. Any tips? Cheers.

library(raster)
library(rgdal)

myshp <- readOGR("Amazon.shp", layer="Amazon")
e <- extent(myshp)
myraster <- raster("Temperature.tif")
myraster.crop <- crop(myraster, e, snap="out", filename="myoutput.tif")
2
rcroprastershapefileclip

2 Answers

48
votes

One option is to use raster::mask()

library(maptools)  ## For wrld_simpl
library(raster)

## Example SpatialPolygonsDataFrame
data(wrld_simpl)
SPDF <- subset(wrld_simpl, NAME=="Brazil")

## Example RasterLayer
r <- raster(nrow=1e3, ncol=1e3, crs=proj4string(SPDF))
r[] <- 1:length(r)

## crop and mask
r2 <- crop(r, extent(SPDF))
r3 <- mask(r2, SPDF)

## Check that it worked
plot(r3)
plot(SPDF, add=TRUE, lwd=2)

enter image description here

0
votes

For simple geometries (i.g. box), the coordinates of the extent can be place directly:

e <- as(extent(c(xmin= -16, xmax= -7.25, ymin= 4, ymax= 12.75)), 'SpatialPolygons')
crs(e) <- "+proj=longlat +datum=WGS84 +no_defs"
r <- crop(my_raster, e)

Source: https://gis.stackexchange.com/questions/229356/crop-a-raster-file-in-r/389376#389376