Do some minor error fixing

These must be very common for this function to be useful. Currently, the only meaningful method is on SpatialPolygons, and it runs rgeos::gIsValid. If FALSE, then it runs a buffer of width 0.

fixErrors(x, objectName, attemptErrorFixes = TRUE,
  useCache = getOption("reproducible.useCache", FALSE), ...)

Arguments

x	Any object that could be fixed for errors. See fixErrors.SpatialPolygons
objectName	Optional. This is only for messaging; if provided, then messages relayed to user will mention this.
attemptErrorFixes	Will attempt to fix known errors. Currently only some failures for SpatialPolygons* are attempted. Notably with raster::buffer(..., width = 0). Default TRUE, though this may not be the right action for all cases.
useCache	Logical, default getOption("reproducible.useCache", FALSE), whether Cache is used on the internal raster::buffer command.
...	Passed to methods. None currently implemented.

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) <- "+init=epsg:4326 +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) <- "+init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
#'
#'
##########
shpEcozonePostProcessed <- postProcess(shpEcozone, studyArea = StudyArea)
#> No cacheRepo supplied. Using value in getOption('reproducible.cachePath')
#>   loading memoised result from previous cropInputs call.
#> Checking for errors in SpatialPolygon
#>   Found no errors.
#> No cacheRepo supplied. Using value in getOption('reproducible.cachePath')
#>   loading memoised result from previous projectInputs call.
#> No cacheRepo supplied. Using value in getOption('reproducible.cachePath')
#>   loading memoised result from previous maskInputs call.
#> Saving output to ./Smallfile12bc71998de6. Specify filename1 or filename2 for more control
#'
# Try manually, individual pieces
shpEcozoneReprojected <- projectInputs(shpEcozone, StudyArea)
shpEcozoneCropped <- cropInputs(shpEcozone, StudyArea)
#>     cropping ...
shpEcozoneClean <- fixErrors(shpEcozone)
#> Checking for errors in SpatialPolygon
#>   Found no errors.
shpEcozoneMasked <- maskInputs(shpEcozone, StudyArea)
#>     intersecting ...
#> Checking for errors in studyArea
#>   Found no errors.

setwd(ow)