Fill NA cells with the nearest cells values

Function to impute a raster object for spatial modeling tools that cannot handle missing values in covariates. The function fill in NA cells with the nearest cells values using a moving window on missing cells. It is an iterative version of the focal function of terra to handle incomplete filling due to isolated NA cells surrounded by other NAs.

Usage

fill_na_near(
  x,
  boundary = NULL,
  fun = mean,
  na.policy = "only",
  na.rm = TRUE,
  start.window = 1,
  ...
)

Arguments

x

A raster layer (SpatRaster or RasterLayer) with missing values to fill in. For multiple rasters (SpatRaster or RasterStack), you can use the combination of lapply() and rast() functions with this function.

boundary

A optional spatial polygon object (spatVector or sf) to be used to mask extra cells outside the study region. It must have the same coordinates reference system (CRS) with the input raster. Defaults to NULL.

fun

A function to compute a value for a cell based on the values of its neighbors. The default is mean. This function must take a vector of values and return a single value (e.g., mean, modal, min or max) or multiple values (e.g., quantile).

na.policy

Character. Specifies which cells to fill. Must be one of "all" (compute for all cells), "only" (only for cells that are NA) or "omit" (skip cells that are NA). The default "only" ensures that only cells that are NA in the input raster are filled.

na.rm

Logical. If TRUE, NA values in the neighborhood are ignored when computing the focal function. The default is TRUE.

start.window

A positive odd integer specifying the starting size of the square focal window. The window will be (2w+1) x (2w+1). The default is 1, which corresponds to a 3x3 start window.

...

Additional arguments passed to the internal focal function. This includes arguments like expand, silent, filename, etc. Note that a custom w (e.g., a weights matrix) cannot be passed via ... as this function's logic is built around an iterative square window.

Value

A SpatRaster object that has all of its NA cells filled in.

Examples

if (FALSE) { # \dontrun{
library(terra)
# Create a sample raster with some NA values
r <- terra::rast(nrows = 10, ncols = 10, res = 1, xmin = 0, ymin = 0)
r[] <- 1:100
r[c(10, 25, 50, 75, 90)] <- NA

# Fill the NAs using the default mean function with 3x3 window
r_filled <- fill_na_near(r)

# Start the filling with a larger 5x5 window
r_filled_large_start <- fill_na_near(r, start.window = 3)

plot(r, main = "Original raster")
plot(r_filled, main = "Filled with mean (3x3 start)")
plot(r_filled_large_start, main = "Filled with mean (5x5 start)")
} # }