focalMultiBand: Apply a spatial filter to a Raster* object
In mqueinnec/foster: Forest Structure Extrapolation with R

Description Usage Arguments Details Value See Also Examples

Apply a spatial filter to a RasterLayer or all layers of a RasterStack or RasterBrick object. The mathematical operation applied within the neighborhood can be done by using a function (fun) or by setting the weights of the matrix w.

focalMultiBand(
  x,
  w,
  fun,
  filename = "",
  na.rm = FALSE,
  pad = FALSE,
  padValue = NA,
  NAonly = FALSE,
  keepNA = TRUE,
  ...
)

`x`	Raster* object or list of Raster* objects.
`w`	Matrix of weights (moving window). A 3x3 windows with weights of 1 would be `w=matrix(1,nr=3,nc=3)` for example.
`fun`	Function (optional). The function should accept a vector of values and return a single number (e.g. mean). It should also accept a `na.rm` argument.
`filename`	Character. Output file name including path to directory and eventually extension. If `x` is a list, `filename` must be a vector of characters with one file name for each element of x. Default is `""` (output not written to disk).
`na.rm`	Logical. If TRUE (default), NAs are removed from computation
`pad`	Logical. IF TRUE, rows and columns are added around `x` to avoid removing border cells.
`padValue`	Numeric. Value of `pad` cells. Usually set to NA and used in combination with `na.rm=TRUE`
`NAonly`	Logical. If TRUE only cell values that are NA are replaced with the computed focal values.
`keepNA`	Logical. If TRUE (default), NA cells of `x` are unchanged
`...`	Additional arguments passed to `writeRaster`

If x contains NA values and na.rm = TRUE is used , using fun or w with weights adjusted to apply equivalent mathematical operation might not produce the same outputs (in that case using weights would give wrong results). See the documentation of focal for more information.

Also, cells of x with NA values might get a non-NA value assigned when located in the neighborhood of non-NA cells and na.rm = TRUE is used. In that case, setting keepNA = TRUE (default) ensures that NA cells of x still have NA values in the output raster.

Raster* object or list of Raster* objects.

focal

# Load raster package
library(raster)

# Open and stack ALS metrics
elev_p95 <- raster(system.file("extdata/examples/ALS_metrics_p95.tif",package="foster"))
cover <- raster(system.file("extdata/examples/ALS_metrics_cov_mean.tif",package="foster"))
Y_vars <- stack(elev_p95,cover)

#Define 3x3 filter with weights of 1
filt <- matrix(1, nrow = 3, ncol = 3)

# Smoothing
Y_vars_smooth <- focalMultiBand(x = Y_vars,
                                w=filt,
                                fun=mean,
                                pad=TRUE,
                                padValue=NA,
                                na.rm=TRUE,
                                keepNA = TRUE)