Extracts the values of cells in a raster (`RasterLayer`

, `RasterStack`

`RasterBrick`

, or `SpatRaster`

) that are covered by polygons in a
simple feature collection (`sf`

or `sfc`

) or `SpatialPolygonsDataFrame`

.
Returns either a summary of the extracted values or the extracted values
themselves.

```
# S4 method for Raster,sf
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for Raster,SpatialPolygonsDataFrame
exact_extract(x, y, ...)
# S4 method for Raster,SpatialPolygons
exact_extract(x, y, ...)
# S4 method for Raster,sfc_MULTIPOLYGON
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for Raster,sfc_POLYGON
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for Raster,sfc_GEOMETRY
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for Raster,sfc_GEOMETRYCOLLECTION
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for SpatRaster,sf
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for SpatRaster,SpatialPolygonsDataFrame
exact_extract(x, y, ...)
# S4 method for SpatRaster,SpatialPolygons
exact_extract(x, y, ...)
# S4 method for SpatRaster,sfc_MULTIPOLYGON
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for SpatRaster,sfc_POLYGON
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for SpatRaster,sfc_GEOMETRY
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
# S4 method for SpatRaster,sfc_GEOMETRYCOLLECTION
exact_extract(
x,
y,
fun = NULL,
...,
weights = NULL,
append_cols = NULL,
coverage_area = FALSE,
default_value = NA_real_,
default_weight = NA_real_,
include_area = FALSE,
include_cell = FALSE,
include_cols = NULL,
include_xy = FALSE,
force_df = FALSE,
full_colnames = FALSE,
stack_apply = FALSE,
summarize_df = FALSE,
quantiles = NULL,
progress = TRUE,
max_cells_in_memory = 3e+07,
grid_compat_tol = 0.001,
colname_fun = NULL
)
```

- x
a

`RasterLayer`

,`RasterStack`

,`RasterBrick`

, or`SpatRaster`

- y
a

`sf`

,`sfc`

,`SpatialPolygonsDataFrame`

, or`SpatialPolygons`

object with polygonal geometries- fun
an optional function or character vector, as described below

- ...
additional arguments to pass to

`fun`

- weights
a weighting raster to be used with the

`weighted_mean`

and`weighted_sum`

summary operations or a user-defined summary function. When`weights`

is set to`'area'`

, the cell areas of`x`

will be calculated and used as weights.- append_cols
when

`fun`

is not`NULL`

, an optional character vector of columns from`y`

to be included in returned data frame.- coverage_area
if

`TRUE`

, output pixel`coverage_area`

instead of`coverage_fraction`

- default_value
an optional value to use instead of

`NA`

in`x`

- default_weight
an optional value to use instead of

`NA`

in`weights`

- include_area
if

`TRUE`

, and`fun`

is`NULL`

, augment the data frame for each feature with a column for the cell area. If the units of the raster CRS are degrees, the area in square meters will be calculated based on a spherical approximation of Earth. Otherwise, a Cartesian area will be calculated (and will be the same for all pixels.) If`TRUE`

and`fun`

is not`NULL`

, add`area`

to the data frame passed to`fun`

for each feature.- include_cell
if

`TRUE`

, and`fun`

is`NULL`

, augment the data frame for each feature with a column for the cell index (`cell`

). If`TRUE`

and`fun`

is not`NULL`

, add`cell`

to the data frame passed to`fun`

for each feature.- include_cols
an optional character vector of column names in

`y`

to be added to the data frame for each feature that is either returned (when`fun`

is`NULL`

) or passed to`fun`

.- include_xy
if

`TRUE`

, and`fun`

is`NULL`

, augment the returned data frame for each feature with columns for cell center coordinates (`x`

and`y`

). If`TRUE`

and`fun`

is not`NULL`

, add`x`

and`y`

to the data frame passed to`fun`

for each feature.- force_df
always return a data frame instead of a vector, even if

`x`

has only one layer and`fun`

has length 1- full_colnames
include the names of

`x`

and`weights`

in the names of the data frame for each feature, even if`x`

or`weights`

has only one layer. This is useful when the results of multiple calls to`exact_extract`

are combined with`cbind`

.- stack_apply
if

`TRUE`

, apply`fun`

independently to each layer or`x`

(and its corresponding layer of`weights`

, if provided.) The number of layers in`x`

and`weights`

must equal each other or`1`

, in which case the single layer raster will be recycled. If`FALSE`

, apply`fun`

to all layers of`x`

(and`weights`

) simultaneously.- summarize_df
pass values, coverage fraction/area, and weights to

`fun`

as a single data frame instead of separate arguments.- quantiles
quantiles to be computed when

`fun = 'quantile'`

- progress
if

`TRUE`

, display a progress bar during processing- max_cells_in_memory
the maximum number of raster cells to load at a given time when using a named summary operation for

`fun`

(as opposed to a function defined using R code). If a polygon covers more than`max_cells_in_memory`

raster cells, it will be processed in multiple chunks.- grid_compat_tol
require value and weight grids to align within

`grid_compat_tol`

times the smaller of the two grid resolutions.- colname_fun
an optional function used to construct column names. Should accept arguments

`values`

(name of value layer),`weights`

(name of weight layer),`fun_name`

(value of`fun`

),`fun_value`

(value associated with`fun`

, for`fun %in% c('quantile', 'frac', 'weighted_frac)`

`nvalues`

(number of value layers),`weights`

(number of weight layers)

a vector, data frame, or list of data frames, depending on the type
of `x`

and the value of `fun`

(see Details)

`exact_extract`

extracts the values of cells in a raster that are covered
by polygonal features in a simple feature collection (`sf`

or `sfc`

) or
`SpatialPolygonDataFrame`

, as well as the fraction or area of each cell that
is covered by the feature. Pixels covered by all parts of the polygon are
considered. If an (invalid) multipart polygon covers the same pixels more
than once, the pixel may have a coverage fraction greater than one.

The function can either return pixel values directly to the caller, or can return the result of a predefined summary operation or user-defined R function applied to the values. These three approaches are described in the subsections below.

If `fun`

is not specified, `exact_extract`

will return a list with
one data frame for each feature in the input feature collection. The data
frame will contain a column with cell values from each layer in the input
raster (and optional weighting raster) and a column indicating
the fraction or area of the cell that is covered by the polygon.

If the input rasters have only one layer, the value and weight columns in the
data frame will be named `values`

or `weights`

. When the input rasters have
more than one layer, the columns will be named according to `names(x)`

and
`names(weights)`

. The column containing pixel coverage will be called
`coverage_fraction`

when `coverage_area = FALSE`

, or `coverage_area`

when
`coverage_area = TRUE`

. Additional columns can be added to the returned data
frames with the `include_area`

, `include_cell`

, and `include_xy`

arguments.

If the output data frames for multiple features are to be combined (e.g.,
with `rbind`

), it may be useful to include identifying column(s) from the
input features in the returned data frames using `include_cols`

.

Often the individual pixel values are not needed; only one or more summary
statistics (e.g., mean, sum) is required for each feature. Common summary
statistics can be calculated by `exact_extract`

directly using a predefined
summary operation. Where possible, this approach is advantageous because it
allows the package to calculate the statistics incrementally, avoiding the
need to store all pixel values in memory at the same time. This allows the
package to process arbitrarily large data with a small amount of memory. (The
`max_pixels_in_memory`

argument can be used to fine-tune the amount of memory
made available to `exact_extract`

.)

To summarize pixel values using a predefined summary option, `fun`

should be
set to a character vector of one or more operation names. If the input raster
has a single layer and a single summary operation is specified,
`exact_extract`

will return a vector with the result of the summary operation
for each feature in the input. If the input raster has multiple layers, or if
multiple summary operations are specified, `exact_extract`

will return a data
frame with a row for each feature and a column for each summary operation /
layer combination. (The `force_df`

option can be used to always return a data
frame instead of a vector.)

The following summary operations are supported:

`min`

- the minimum non-`NA`

value in any raster cell wholly or partially covered by the polygon`max`

- the maximum non-`NA`

value in any raster cell wholly or partially covered by the polygon`count`

- the sum of fractions of raster cells with non-`NA`

values covered by the polygon`sum`

- the sum of non-`NA`

raster cell values, multiplied by the fraction of the cell that is covered by the polygon`mean`

- the mean cell value, weighted by the fraction of each cell that is covered by the polygon`median`

- the median cell value, weighted by the fraction of each cell that is covered by the polygon`quantile`

- arbitrary quantile(s) of cell values, specified in`quantiles`

, weighted by the fraction of each cell that is covered by the polygon`mode`

- the most common cell value, weighted by the fraction of each cell that is covered by the polygon. Where multiple values occupy the same maximum number of weighted cells, the largest value will be returned.`majority`

- synonym for`mode`

`minority`

- the least common cell value, weighted by the fraction of each cell that is covered by the polygon. Where multiple values occupy the same minimum number of weighted cells, the smallest value will be returned.`variety`

- the number of distinct values in cells that are wholly or partially covered by the polygon.`variance`

- the population variance of cell values, weighted by the fraction of each cell that is covered by the polygon.`stdev`

- the population standard deviation of cell values, weighted by the fraction of each cell that is covered by the polygon.`coefficient_of_variation`

- the population coefficient of variation of cell values, weighted by the fraction of each cell that is covered by the polygon.`weighted_mean`

- the mean cell value, weighted by the product of the fraction of each cell covered by the polygon and the value of a second weighting raster provided as`weights`

`weighted_sum`

- the sum of defined raster cell values, multiplied by the fraction of each cell that is covered by the polygon and the value of a second weighting raster provided as`weights`

`weighted_stdev`

- the population standard deviation of cell values, weighted by the product of the fraction of each cell covered by the polygon and the value of a second weighting raster provided as`weights`

`weighted_variance`

- the population variance of cell values, weighted by the product of the fraction of each cell covered by the polygon and the value of a second weighting raster provided as`weights`

`frac`

- returns one column for each possible value of`x`

, with the the fraction of defined raster cells that are equal to that value.`weighted_frac`

- returns one column for each possible value of`x`

, with the fraction of defined cells that are equal to that value, weighted by`weights.`

In all of the summary operations, `NA`

values in the the primary raster (`x`

)
raster are ignored (i.e., `na.rm = TRUE`

.) If `NA`

values occur in the
weighting raster, the result of the weighted operation will be `NA`

. `NA`

values in both `x`

and `weights`

can be replaced on-the-fly using the
`default_value`

and `default_weight`

arguments.

If no predefined summary operation is suitable, a user-defined R function may
be provided as `fun`

. The function will be called once for each feature and
must return either a single value or a data frame. The results of the
function for each feature will be combined and returned by `exact_extract`

.

The simplest way to write a summary function is to set
argument `summarize_df = TRUE`

. (For backwards compatibility, this is not the
default.) In this mode, the summary function takes the signature
`function(df, ...)`

where `df`

is the same data frame that would be returned
by `exact_extract`

with `fun = NULL`

.

With `summarize_df = FALSE`

, the function must have the signature
`function(values, coverage_fractions, ...)`

when weights are not used, and
`function(values, coverage_fractions, weights, ...)`

when weights are used.
If the value and weight rasters each have a single layer, the function arguments
will be vectors; if either has multiple layers, the function arguments will
be data frames, with column names taken from the names of the value/weight
rasters. Values brought in through the `include_xy`

, `include_area`

,
`include_cell`

, and `include_cols`

arguments will be added to the `values`

data frame. For most applications, it is simpler to set `summarize_df = TRUE`

and work with all inputs in a single data frame.

```
rast <- raster::raster(matrix(1:100, ncol=10), xmn=0, ymn=0, xmx=10, ymx=10)
poly <- sf::st_as_sfc('POLYGON ((2 2, 7 6, 4 9, 2 2))')
# named summary operation on RasterLayer, returns vector
exact_extract(rast, poly, 'mean')
#> [1] 43.16667
# two named summary operations on RasterLayer, returns data frame
exact_extract(rast, poly, c('min', 'max'))
#> min max
#> 1 25 65
# named summary operation on RasterStack, returns data frame
stk <- raster::stack(list(a=rast, b=sqrt(rast)))
exact_extract(stk, poly, 'mean')
#> mean.a mean.b
#> 1 43.16667 6.525083
# named weighted summary operation, returns vector
weights <- raster::raster(matrix(runif(100), ncol=10), xmn=0, ymn=0, xmx=10, ymx=10)
exact_extract(rast, poly, 'weighted_mean', weights=weights)
#> [1] 43.04758
# custom summary function, returns vector
exact_extract(rast, poly, function(value, cov_frac) length(value[cov_frac > 0.9]))
#> [1] 7
```