Extract values from a SpatRaster

Extract values from a SpatRaster for a set of locations. The locations can be a SpatVector (points, lines, polygons), a data.frame or matrix with (x, y) or (longitude, latitude – in that order!) coordinates, or a vector with cell numbers.

When argument y is a SpatVector the first column has the ID (record number) of the SpatVector used (unless you set ID=FALSE).

Alternatively, you can use zonal after using rasterize with a SpatVector (this may be more efficient in some cases).

Usage

# S4 method for class 'SpatRaster,SpatVector'
extract(x, y, fun=NULL, method="simple", cells=FALSE, xy=FALSE,
    ID=TRUE, weights=FALSE, exact=FALSE, touches=is.lines(y), small=TRUE,
  layer=NULL, bind=FALSE, raw=FALSE, search_radius=0, ...)

# S4 method for class 'SpatRaster,SpatExtent'
extract(x, y, cells=FALSE, xy=FALSE)

# S4 method for class 'SpatRaster,matrix'
extract(x, y, cells=FALSE, method="simple")

# S4 method for class 'SpatRaster,numeric'
extract(x, y, xy=FALSE, raw=FALSE)

# S4 method for class 'SpatVector,SpatVector'
extract(x, y)

Arguments

x: SpatRaster or SpatVector of polygons
y: SpatVector (points, lines, or polygons). Alternatively, for points, a 2-column matrix or data.frame (x, y) or (lon, lat). Or a vector with cell numbers
fun: function to summarize the extracted data by line or polygon geometry. You can use fun=table to tabulate raster values for each line or polygon geometry. If weights=TRUE or exact=TRUE only mean, sum, min, max and table are accepted). Ignored if y has point geometry
method: character. method for extracting values with points ("simple" or "bilinear"). With "simple" values for the cell a point falls in are returned. With "bilinear" the returned values are interpolated from the values of the four nearest raster cells
cells: logical. If TRUE the cell numbers are also returned, unless fun is not NULL. Also see cells
xy: logical. If TRUE the coordinates of the cells are also returned, unless fun is not NULL. See xyFromCell
ID: logical. Should an ID column be added? If so, the first column returned has the IDs (record numbers) of y
weights: logical. If TRUE and y has polygons, the approximate fraction of each cell that is covered is returned as well, for example to compute a weighted mean
exact: logical. If TRUE and y has polygons, the exact fraction of each cell that is covered is returned as well, for example to compute a weighted mean
touches: logical. If TRUE, values for all cells touched by lines or polygons are extracted, not just those on the line render path, or whose center point is within the polygon. Not relevant for points; and always considered TRUE when weights=TRUE or exact=TRUE
small: logical. If TRUE, values for all cells in touched polygons are extracted if none of the cells center points is within the polygon; even if touches=FALSE
layer: character or numeric to select the layer to extract from for each geometry. If layer is a character it can be a name in y or a vector of layer names. If it is numeric, it must be integer values between 1 and nlyr(x)
bind: logical. If TRUE, a SpatVector is returned consisting of the input SpatVector y and the cbind-ed extracted values
raw: logical. If TRUE, a matrix is returned with the "raw" numeric cell values. If FALSE, a data.frame is returned and the cell values are transformed to factor, logical, or integer values, where appropriate
search_radius: positive number. A search-radius that is used when y has point geometry. If this value is larger than zero, it is the maximum distance used to find the a cell with a value that is nearest to the cell that the point falls in if that cell that has a missing (NA) value. The value of this nearest cell, the distance to the original cell, and the new cell number are returned. The radius should be expressed in m if the data have lon/lat coordinates or in the distance unit of the crs in other cases (typically also m). For lon/lat data, the mean latitude of the points is used to compute the distances, so this may be imprecise for data with a large latitudinal range
...: additional arguments to fun if y is a SpatVector. For example na.rm=TRUE. Or arguments passed to the SpatRaster,SpatVector method if y is a matrix (such as the method and cells arguments)

Value

data.frame, matrix or SpatVector

Examples

r <- rast(ncols=5, nrows=5, xmin=0, xmax=5, ymin=0, ymax=5)
values(r) <- 1:25
xy <- rbind(c(0.5,0.5), c(2.5,2.5))
p <- vect(xy, crs="+proj=longlat +datum=WGS84")

extract(r, xy)
#>   lyr.1
#> 1    21
#> 2    13
extract(r, p)
#>   ID lyr.1
#> 1  1    21
#> 2  2    13

r[1,]
#>   lyr.1
#> 1     1
#> 2     2
#> 3     3
#> 4     4
#> 5     5
r[5]
#>   lyr.1
#> 1     5
r[,5]
#>   lyr.1
#> 1     5
#> 2    10
#> 3    15
#> 4    20
#> 5    25

r[c(0:2, 99:101)]
#>   lyr.1
#> 1     1
#> 2     2
#> 3    NA
#> 4    NA
#> 5    NA

f <- system.file("ex/meuse.tif", package="terra")
r <- rast(f)

xy <- cbind(179000, 330000)
xy <- rbind(xy-100, xy, xy+1000)
extract(r, xy)
#>   meuse
#> 1   378
#> 2   251
#> 3   208

p <- vect(xy)
g <- geom(p)
g
#>      geom part      x      y hole
#> [1,]    1    1 178900 329900    0
#> [2,]    2    1 179000 330000    0
#> [3,]    3    1 180000 331000    0

extract(r, p)
#>   ID meuse
#> 1  1   378
#> 2  2   251
#> 3  3   208

x <- r + 10
extract(x, p)
#>   ID meuse
#> 1  1   388
#> 2  2   261
#> 3  3   218

i <- cellFromXY(r, xy)
x[i]
#>   meuse
#> 1   388
#> 2   261
#> 3   218
r[i]
#>   meuse
#> 1   378
#> 2   251
#> 3   208

y <- c(x,x*2,x*3)
y[i]
#>   meuse meuse meuse
#> 1   388   776  1164
#> 2   261   522   783
#> 3   218   436   654

## extract with a polygon
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
v <- v[1:2,]

rf <- system.file("ex/elev.tif", package="terra")
x <- rast(rf)
extract(x, v, mean, na.rm=TRUE)
#>   ID elevation
#> 1  1  467.1052
#> 2  2  333.8629

z <- rast(v, resolution=.1, names="test")
values(z) <- 1:ncell(z)
e <- extract(z, v, ID=TRUE)
e
#>   ID test
#> 1  1    2
#> 2  1    3
#> 3  1    6
#> 4  1    7
#> 5  1    8
#> 6  2   13
#> 7  2   17
#> 8  2   18
#> 9  2   19
tapply(e[,2], e[,1], mean, na.rm=TRUE)
#>     1     2 
#>  5.20 16.75 

x <- c(z, z*2, z/3)
names(x) <- letters[1:3]

e <- extract(x, v, ID=TRUE)
de <- data.frame(e)
aggregate(de[,2:4], de[,1,drop=FALSE], mean)
#>   ID     a    b        c
#> 1  1  5.20 10.4 1.733333
#> 2  2 16.75 33.5 5.583333

Extract values from a SpatRaster

Usage

Arguments

Value

See also

Examples