How to extract values from rasterstack with xy coordinates?
I have a rasterstack (5 raster layers) that actually is a time series raster.
r <- raster(nrow=20, ncol=200)
s <- stack( sapply(1:5, function(i) setValues(r, rnorm(ncell(r), i, 3) )) )
s
class : RasterStack
dimensions : 20, 200, 4000, 5 (nrow, ncol, ncell, nlayers)
resolution : 1.8, 9 (x, y)
extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
names : layer.1, layer.2, layer.3, layer.4, layer.5
min values : -9.012146, -9.165947, -9.707269, -7.829763, -5.332007
max values : 11.32811, 11.97328, 15.99459, 15.66769, 16.72236
My objective is to plot each pixel and explore their behavior over time.
How could I extract each pixels together with their x,y coordinates and plot a time series curve?
Answer
You can use extract and pass a vector of cell numbers you wish to extract to return a matrix of values in each pixel. Each row represents a pixel, the columns are layers...
mat <- extract( s , 1:ncell(s) )
head( mat )
# layer.1 layer.2 layer.3 layer.4 layer.5
#[1,] -0.2138718 3.114061 3.670945 1.2560295 2.881104
#[2,] 3.3580783 5.008205 2.315353 2.3247236 11.539837
#[3,] 3.2173875 2.958985 1.055389 3.1016730 4.064339
#[4,] 4.1113162 4.469828 3.113790 8.5329679 8.771459
#[5,] -2.4011283 4.747527 4.299707 2.2111643 9.457012
#[6,] -2.6159294 5.659211 1.926900 -0.3886837 5.661419
However extract is more useful when trying to get particular pixels. To get all pixels with the x / y coordinates you can just use rasterToPoints...
head( rasterToPoints( s ) )
# x y layer.1 layer.2 layer.3 layer.4 layer.5
#[1,] -179.1 85.5 -0.2138718 3.114061 3.670945 1.2560295 2.881104
#[2,] -177.3 85.5 3.3580783 5.008205 2.315353 2.3247236 11.539837
#[3,] -175.5 85.5 3.2173875 2.958985 1.055389 3.1016730 4.064339
#[4,] -173.7 85.5 4.1113162 4.469828 3.113790 8.5329679 8.771459
#[5,] -171.9 85.5 -2.4011283 4.747527 4.299707 2.2111643 9.457012
#[6,] -170.1 85.5 -2.6159294 5.659211 1.926900 -0.3886837 5.661419