How to extract raster values from a RasterStackTS object using a shapefile?

Question

I have a rasterstack and I need to extract the values from every raster using a shapefile.

I know it's very easy with a "normal" rasterstack, but I have a RasterStackTS object. Unfortunately I must manage a RasterStackTS object, because I've obtained if from a previous computation.

Here a reproducible example, taken from Babak Naimi's website.

library(rts)

# location of files
path <- system.file("external", package="rts")

# list of raster files:
lst <- list.files(path=path,pattern='.asc$',full.names=TRUE)

lst

#create a random shapefile over the raster extent
r_4_shp<- raster(lst[1])
shp <- rasterToPolygons(r_4_shp, fun=function(x){x>0.77})

#visualize the shp over the raster
plot(r_4_shp)
plot(shp, add=T)

# creating a RasterStack object
r <- stack(lst)

# corresponding dates to 4 rasters
d <- c("2000-02-01","2000-03-01","2000-04-01","2000-05-01") 

d <- as.Date(d)



# creating a RasterStackTS object:
rt <- rts(r,d)

rt

#try to extract raster values with the shapefile
sp_basin_mean <- extract(rt, shp)

I tried `extract(rt, shp, time = d[1])` and it creates a corrupt object. Interesting. — Roman Luštrik, Jul 17 '15 at 09:18
Right...and the error I get from extract(rt, shp) is "subscript out of bounds". — FraNut, Jul 17 '15 at 09:39
`t(x@raster[i, drop=drop])` in [this line](https://github.com/cran/rts/blob/master/R/extract.R#L31) "tilts" the data to have only one row, and rows 1:4 are of course not subsettable. — Roman Luštrik, Jul 17 '15 at 11:01
That means I should apply the extract function layer by layer using a for loop? — FraNut, Jul 17 '15 at 15:14

score 0 · Answer 1 · edited May 23 '17 at 10:26

0

I found the answer here. Most of the raster functions cannot work with a RasterStackTS object. However the raster object is kept in slot @raster. Indeed this line runs, using the data from the example I've posted before:

sp_basin_mean <- extract(rt@raster, shp)

edited May 23 '17 at 10:26

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answered Oct 07 '15 at 18:00

FraNut

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How to extract raster values from a RasterStackTS object using a shapefile?

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