This function can be used to mask inputs from data. Masking here is equivalent to raster::mask (though fastMask is used here) or raster::intersect.

maskInputs(x, studyArea, ...)

# S3 method for Raster
maskInputs(
  x,
  studyArea,
  rasterToMatch,
  maskWithRTM = NULL,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

# S3 method for Spatial
maskInputs(
  x,
  studyArea,
  rasterToMatch,
  maskWithRTM = FALSE,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

# S3 method for sf
maskInputs(x, studyArea, verbose = getOption("reproducible.verbose", 1), ...)

Arguments

x

An object to do a geographic raster::mask/raster::intersect. See methods.

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.

...

Passed to methods. None currently implemented.

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.

maskWithRTM

Logical. If TRUE, then the default,

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

Examples

# Add a study area to Crop and Mask to # Create a "study area" library(sp) library(raster) ow <- setwd(tempdir()) # 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) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0" ########## shpEcozonePostProcessed <- postProcess(shpEcozone, studyArea = StudyArea)
#> No cacheRepo supplied and getOption('reproducible.cachePath') is inside a temporary directory; #> this will not persist across R sessions.
#> ...(Object to retrieve (1ca251f991c47008.rds))
#> loaded cached result from previous cropInputs call,
#> Checking for errors in SpatialPolygon
#> Found no errors.
#> No cacheRepo supplied and getOption('reproducible.cachePath') is inside a temporary directory; #> this will not persist across R sessions.
#> ...(Object to retrieve (b8053bfec9665f45.rds))
#> loaded cached result from previous projectInputs call,
#> Checking for errors in SpatialPolygon
#> Found no errors.
#> No cacheRepo supplied and getOption('reproducible.cachePath') is inside a temporary directory; #> this will not persist across R sessions.
#> ...(Object to retrieve (51007a91ef41d8db.rds))
#> loaded cached result from previous maskInputs call,
#> Skipping writeOutputs; filename2 is NULL
# Try manually, individual pieces shpEcozoneReprojected <- projectInputs(shpEcozone, StudyArea)
#> reprojecting ...
shpEcozoneCropped <- cropInputs(shpEcozone, StudyArea)
#> cropping ...
#> useGDAL is TRUE, but problem is small enough for RAM; skipping GDAL; useGDAL = 'force' to override
#> Checking for errors in SpatialPolygon
#> Found no errors.
#> although coordinates are longitude/latitude, st_intersection assumes that they are planar
shpEcozoneClean <- fixErrors(shpEcozone)
#> Checking for errors in SpatialPolygon
#> Found no errors.
shpEcozoneMasked <- maskInputs(shpEcozone, StudyArea)
#> Checking for errors in SimpleFeature
#> Found no errors.
#> maskInputs with sf class objects is still experimental
#> intersecting ...
#> Checking for errors in SimpleFeature
#> Found no errors.
#> although coordinates are longitude/latitude, st_intersection assumes that they are planar
#> dist is assumed to be in decimal degrees (arc_degrees).
setwd(ow)