Crop a Spatial* or Raster* object

This function can be used to crop or reproject module inputs from raw data.

cropInputs(
  x,
  studyArea,
  rasterToMatch,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

# S3 method for default
cropInputs(x, studyArea, rasterToMatch, ...)

# S3 method for spatialClasses
cropInputs(
  x,
  studyArea = NULL,
  rasterToMatch = NULL,
  verbose = getOption("reproducible.verbose", 1),
  extentToMatch = NULL,
  extentCRS = NULL,
  useGDAL = getOption("reproducible.useGDAL", FALSE),
  useCache = getOption("reproducible.useCache", FALSE),
  ...
)

# S3 method for sf
cropInputs(
  x,
  studyArea = NULL,
  rasterToMatch = NULL,
  verbose = getOption("reproducible.verbose", 1),
  extentToMatch = NULL,
  extentCRS = NULL,
  useCache = getOption("reproducible.useCache", FALSE),
  ...
)

Arguments

x

A Spatial*, sf, or Raster* object.

studyArea

SpatialPolygons* object used for masking and possibly cropping if no rasterToMatch is provided. If not in same CRS, then it will be spTransformed to CRS of x before masking. Currently, this function will not reproject the x. Optional in postProcess.

rasterToMatch

Template Raster* object used for cropping (so extent should be the extent of desired outcome) and reprojecting (including changing the resolution and projection). See details in postProcess().

verbose

Numeric, -1 silent (where possible), 0 being very quiet, 1 showing more messaging, 2 being more messaging, etc. Default is 1. Above 3 will output much more information about the internals of Caching, which may help diagnose Caching challenges. Can set globally with an option, e.g., options('reproducible.verbose' = 0) to reduce to minimal

...

Passed to raster::crop

extentToMatch

Optional. Can pass an extent here and a crs to extentCRS instead of rasterToMatch. These will override rasterToMatch, with a warning if both passed.

extentCRS

Optional. Can pass a crs here with an extent to extentTomatch instead of rasterToMatch

useGDAL

Logical or "force". This is defunct; internals now can use terra if options("reproducible.useTerra" = TRUE), which is not (yet) the default.

useCache

Logical, default getOption("reproducible.useCache", FALSE), whether Cache is used internally.

Value

A GIS file (e.g., RasterLayer, SpatRaster etc.) that has been appropriately cropped.

Author

Eliot McIntire, Jean Marchal, Ian Eddy, and Tati Micheletti

Examples

library(sp)
library(raster)

# make a SpatialPolygon
coords1 <- structure(c(-123.98, -117.1, -80.2, -100, -123.98, 60.9, 67.73, 65.58, 51.79, 60.9),
                       .Dim = c(5L, 2L))
Sr1 <- Polygon(coords1)
Srs1 <- Polygons(list(Sr1), "s1")
shpEcozone <- SpatialPolygons(list(Srs1), 1L)
crs(shpEcozone) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"

# make a "study area" that is subset of larger dataset
coords <- structure(c(-118.98, -116.1, -99.2, -106, -118.98, 59.9, 65.73, 63.58, 54.79, 59.9),
                      .Dim = c(5L, 2L))
Sr1 <- Polygon(coords)
Srs1 <- Polygons(list(Sr1), "s1")
StudyArea <- SpatialPolygons(list(Srs1), 1L)
crs(StudyArea) <- crs(shpEcozone)
projString <- "+proj=utm +zone=15 +ellps=GRS80 +datum=NAD83 +units=m +no_defs"
StudyArea <- sp::spTransform(StudyArea, CRSobj = projString)
cropInputs(shpEcozone, StudyArea)
#>     cropping ...
#> class       : SpatialPolygonsDataFrame 
#> features    : 1 
#> extent      : -122.0839, -97.85564, 54.83759, 67.31711  (xmin, xmax, ymin, ymax)
#> crs         : +proj=longlat +datum=WGS84 +no_defs 
#> variables   : 0