st_apply: st_apply apply a function to one or more array dimensions

In stars: Spatiotemporal Arrays, Raster and Vector Data Cubes

st_apply apply a function to one or more array dimensions

Description

st_apply apply a function to array dimensions: aggregate over space, time, or something else

Usage

## S3 method for class 'stars'
st_apply(
  X,
  MARGIN,
  FUN,
  ...,
  CLUSTER = NULL,
  PROGRESS = FALSE,
  FUTURE = FALSE,
  rename = TRUE,
  .fname,
  single_arg = has_single_arg(FUN, list(...)) || can_single_arg(FUN),
  keep = FALSE
)

Arguments

X	object of class stars
MARGIN	see apply; index number(s) or name(s) of the dimensions over which FUN will be applied
FUN	see apply and see Details.
...	arguments passed on to FUN
CLUSTER	cluster to use for parallel apply; see makeCluster
PROGRESS	logical; if TRUE, use pbapply::pbapply to show progress bar
FUTURE	logical;if TRUE, use future.apply::future_apply
rename	logical; if TRUE and X has only one attribute and FUN is a simple function name, rename the attribute of the returned object to the function name
.fname	function name for the new attribute name (if one or more dimensions are reduced) or the new dimension (if a new dimension is created); if missing, the name of FUN is used
single_arg	logical; if TRUE, FUN takes a single argument (like fn_ndvi1 below), if FALSE FUN takes multiple arguments (like fn_ndvi2 below).
keep	logical; if TRUE, preserve dimension metadata (e.g. time stamps)

Details

FUN is a function which either operates on a single object, which will be the data of each iteration step over dimensions MARGIN, or a function that has as many arguments as there are elements in such an object. See the NDVI examples below. The second form can be VERY much faster e.g. when a trivial function is not being called for every pixel, but only once (example).

The heuristics for the default of single_arg work often, but not always; try setting this to the right value when st_apply gives an error.

Value

object of class stars with accordingly reduced number of dimensions; in case FUN returns more than one value, a new dimension is created carrying the name of the function used; see the examples. Following the logic of apply, This new dimension is put before the other dimensions; use aperm to rearrange this, see last example.

Examples

tif = system.file("tif/L7_ETMs.tif", package = "stars")
x = read_stars(tif)
st_apply(x, 1:2, mean) # mean band value for each pixel
st_apply(x, c("x", "y"), mean) # equivalent to the above
st_apply(x, 3, mean)   # mean of all pixels for each band
## Not run: 
 st_apply(x, "band", mean) # equivalent to the above
 st_apply(x, 1:2, range) # min and max band value for each pixel
 fn_ndvi1 = function(x) (x[4]-x[3])/(x[4]+x[3]) # ONE argument: will be called for each pixel
 fn_ndvi2 = function(red,nir) (nir-red)/(nir+red) # n arguments: will be called only once
 ndvi1 = st_apply(x, 1:2, fn_ndvi1)
   # note that we can select bands 3 and 4 in the first argument:
 ndvi2 = st_apply(x[,,,3:4], 1:2, fn_ndvi2) 
 all.equal(ndvi1, ndvi2)
 # compute the (spatial) variance of each band; https://github.com/r-spatial/stars/issues/430
 st_apply(x, 3, function(x) var(as.vector(x))) # as.vector is required!
 # to get a progress bar also in non-interactive mode, specify:
 if (require(pbapply)) { # install it, if FALSE
   pboptions(type = "timer")
 }
 st_apply(x, 1:2, range) # dimension "range" is first; rearrange by:
 st_apply(x, 1:2, range) %>% aperm(c(2,3,1))

## End(Not run)

stars documentation built on Sept. 11, 2023, 5:10 p.m.