exactextractr (version 0.4.0)

exact_extract: Extract or summarize values from Raster* objects

Description

Extracts the values of cells in a Raster* that are covered by a simple feature collection containing polygonal geometries, as well as the fraction of each cell that is covered by the polygon. Returns either the result of a summary operation or function applied to the values and coverage fractions (if fun is specified), or a data frame containing the values and coverage fractions themselves (if fun is NULL.)

Usage

# S4 method for Raster,sf
exact_extract(
  x,
  y,
  fun = NULL,
  ...,
  include_xy = FALSE,
  progress = TRUE,
  max_cells_in_memory = 3e+07,
  include_cell = FALSE
)
# S4 method for Raster,sfc_MULTIPOLYGON
exact_extract(
  x,
  y,
  fun = NULL,
  ...,
  weights = NULL,
  include_xy = FALSE,
  progress = TRUE,
  max_cells_in_memory = 3e+07,
  include_cell = FALSE
)
# S4 method for Raster,sfc_POLYGON
exact_extract(
  x,
  y,
  fun = NULL,
  ...,
  weights = NULL,
  include_xy = FALSE,
  progress = TRUE,
  max_cells_in_memory = 3e+07,
  include_cell = FALSE
)
# S4 method for Raster,sfc_GEOMETRY
exact_extract(
  x,
  y,
  fun = NULL,
  ...,
  weights = NULL,
  include_xy = FALSE,
  progress = TRUE,
  max_cells_in_memory = 3e+07,
  include_cell = FALSE
)

Arguments

x

a RasterLayer, RasterStack, or RasterBrick

y

a sf object with polygonal geometries

fun

an optional function or character vector, as described below

...

additional arguments to pass to fun

include_xy

if TRUE, augment the returned data frame with columns for cell center coordinates (x and y) or pass them to fun

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.

include_cell

if TRUE, augment the returned data frame with column for cell index

weights

a weighting raster to be used with the weighted_mean and weighted_sum summary operations.

Value

a vector or list of data frames, depending on the type of x and the value of fun (see Details)

Details

The value of fun may be set to a string (or vector of strings) representing summary operations supported by the exactextract library. 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 following summary operations are supported:

• min - the minimum defined value in any raster cell wholly or partially covered by the polygon

• max - the maximum defined value in any raster cell wholly or partially covered by the polygon

• count - the sum of fractions of raster cells with defined values covered by the polygon

• sum - the sum of defined 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

• 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

Alternatively, an R function may be provided as fun. The function will be called for each feature with with vectors of cell values and weights as arguments. exact_extract will then return a vector of the return values of fun.

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 values from each layer in the input `Raster*`, and a final column indicating the fraction of the cell that is covered by the polygon.

Examples

# NOT RUN {
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')

# two named summary operations on RasterLayer, returns data frame
exact_extract(rast, poly, c('min', 'max'))

# named summary operation on RasterStack, returns data frame
stk <- raster::stack(list(a=rast, b=sqrt(rast)))
exact_extract(stk, poly, 'mean')

# 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)

# custom summary function, returns vector
exact_extract(rast, poly, function(value, cov_frac) length(value[cov_frac > 0.9]))

# }