export: Export spatial data from MPG and GOC models

In achubaty/grainscape: Landscape Connectivity, Habitat, and Protected Area Networks

Export spatial data from MPG and GOC models

Description

This function automates the export of raster and vector spatial data from mpg and grain objects. By default it places them in a new directory, unless an existing one is specified with overwrite = TRUE.

It can also be used to process mpg and grain objects to produce R spatial objects that are convenient for plotting or analysis within R. Use R = TRUE in which case all parameters related to file export are ignored. (Default R = FALSE)

The raster::writeRaster() is used for rasters, and sf::st_write() is used to export ESRI compatible shape files.

Usage

export(
  x,
  dirname = NULL,
  path = ".",
  rasterFormat = "GTiff",
  overwrite = FALSE,
  R = FALSE,
  vorBound = FALSE,
  ...
)

## S4 method for signature 'mpg'
export(
  x,
  dirname = NULL,
  path = ".",
  rasterFormat = "GTiff",
  overwrite = FALSE,
  R = FALSE,
  vorBound = FALSE,
  ...
)

## S4 method for signature 'grain'
export(
  x,
  dirname = NULL,
  path = ".",
  rasterFormat = "GTiff",
  overwrite = FALSE,
  R = FALSE,
  vorBound = FALSE,
  ...
)

## S4 method for signature 'goc'
export(
  x,
  dirname = NULL,
  path = ".",
  rasterFormat = "GTiff",
  overwrite = FALSE,
  R = FALSE,
  vorBound = FALSE,
  ...
)

Arguments

x	A mpg or grain object
dirname	The name of a new directory to create. If NULL a directory with a name containing the date and time will be created.
path	A path to where this new directory dirname should be created. Defaults to the working directory.
rasterFormat	The format for exported rasters. See writeFormats() for options. Defaults to GeoTiff (rasterFormat='GTiff'). Use rasterFormat='raster' to save .grd files in native raster package format.
overwrite	If directory already exists will overwrite existing files inside. Defaults to FALSE.
R	If TRUE, return the spatial objects that would be written to files. Do not write these files and ignore dirname, path, rasterFormat, overwrite parameters. This is useful for visualization using R plotting functions, or spatial analysis within R. Defaults to FALSE
vorBound	Specify whether to create a raster with the boundaries of the Voronoi polygons ⁠=1⁠ and the remainder ⁠=NA⁠. This may be useful for visualizing relationships among polygons in a grain of connectivity. This can add time to the export on very large rasters. Defaults to FALSE.
...	Additional arguments (not used).

Value

Invisibly returns the path to the folder created.

Side effect of exporting files representing raster and vector spatial data in the object.

Please note that for vector data export the attribute name is limited to 8 characters in shape files. See the tables below for the abbreviations used and their meaning.

Exported from mpg objects:

nodes, linksCentroid, linksPerim are shape files giving the locations of the patch centroids, links among centroids, and links among perimeters of patches respectively. ⁠patchId, voronoi⁠ are rasters giving the patch identifier of the patch, or of the patch that the Voronoi polygon refers to. ⁠lcpPerimWeight, lcpLinkId⁠ give the weight in cost surface units of the shortest paths between perimeters, and the identifiers of those links respectively. vorBound gives the boundaries of the Voronoi polygons (if specified).

Description of node (vertex) and link (edge) weights in mpg objects and their corresponding attribute names in the shape files created.

type	MPG name	SHP name	Description
node	patchId	patchId	Patch ID from patchId raster
node	patchArea	patchA	Area of patch
node	patchEdgeArea	patchEA	Edge area of patch
node	coreArea	coreA	Area excluding edge of patch
node	centroidX	ctrX	Centroid of the patch (X)
node	centroidY	ctrY	Centroid of the patch (Y)
link	e1	e1	Id of first patch at end of link
link	e2	e2	Id of second patch at end of link
link	linkId	linkId	Link ID from lcpLinkId raster
link	lcPerimWeight	lcpPerWt	Cost length of link from patch perimeters
link	startPerimX	strtPerX	Coordinate of link endpoint on first patch (X)
link	startPerimY	strtPerY	Coordinate of link endpoint on first patch (Y)
link	endPerimX	endPerX	Coordinate of link endpoint on second patch (X)
link	endPerimY	endPerY	Coordinate of link endpoint on second patch (Y)

Exported from grain objects:

⁠nodes, linksCentroid⁠ are shape files giving the locations of the Voronoi polygon centroids and links among them respectively. voronoi are rasters gives the polygon identifier of each cluster of patches. vorBound gives the boundaries of the Voronoi polygons (if specified).

Description of node (vertex) and link (edge) weights in grain objects and their corresponding attribute names in the shape files created.

Type	GOC name	SHP name	Description
node	polygonId	polyId	Polygon ID from grain voronoi raster
node	polygonArea	polyA	Area of polygon from grain voronoi raster
node	totalPatchArea	patchA	Total area of all patches in polygon
node	totalPatchEdgeArea	patchEA	Total area of all patch edges in polygon
node	totalCoreArea	coreA	Total area of patches in polygon excluding edges
node	centroidX	ctrX	Centroid of the polygon (X)
node	centroidY	ctrY	Centroid of the polygon (Y)
link	e1	e1	ID of first patch at end of link
link	e2	e2	ID of second patch at end of link
link	maxWeight	maxWt	The maximum weight of all links connecting patches between polygons
link	linkIdMaxWeight	maxWt	The link id of that maximum weight link (lcpLinkId)
link	minWeight	min	The minimum weight of all links connecting patches between polygons
link	linkIdMinWeight	minWt	The link id of that minimum weight link (lcpLinkId)
link	medianWeight	medWt	The median weight of all links connecting patches between polygons
link	meanWeight	meanWT	The minimum weight of all links connecting patches between polygons
link	numlinksWeight	numEWt	The number of links connecting patches between polygons
link	eucCentroidWeight	eucCtrWt	The Euclidean distance between centroids of polygons

Author(s)

Paul Galpern and Alex Chubaty

See Also

MPG(), GOC(), grain()

Examples

## Load raster landscape
tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape"))

## Create a resistance surface from a raster using an is-becomes reclassification
tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12)))
## Produce a patch-based MPG where patches are resistance features=1
tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1)
## Extract a representative subset of 5 grains of connectivity
tinyPatchGOC <- GOC(tinyPatchMPG, nThresh = 5)
## Export rasters and vectors and place in an R object
sp_tinyPatchGOC <- export(grain(tinyPatchGOC, 2), R = TRUE)  # nolint
sp_tinyPatchMPG <- export(tinyPatchMPG, R = TRUE) # nolint

## Export raster and vectors to a specified directory
exportPath <- tempdir()
export(grain(tinyPatchGOC, 2), dirname = "tiny_goc_thresh2", path = exportPath)
export(tinyPatchMPG, dirname = "tiny_mpg", path = exportPath, vorBound = TRUE)

## clean up
unlink(file.path(exportPath, "tiny_goc_thresh2"), recursive = TRUE)
unlink(file.path(exportPath, "tiny_mpg"), recursive = TRUE)

achubaty/grainscape documentation built on Jan. 4, 2025, 8:43 a.m.