export: Export spatial data from MPG and GOC models
In grainscape: Landscape Connectivity, Habitat, and Protected Area Networks
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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)
grainscape documentation built on April 20, 2023, 9:12 a.m.
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| export | R Documentation |
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 |
dirname |
The name of a new directory to create. If |
path |
A path to where this new directory |
rasterFormat |
The format for exported rasters. See |
overwrite |
If directory already exists will overwrite existing files inside.
Defaults to |
R |
If |
vorBound |
Specify whether to create a raster with the boundaries of
the Voronoi polygons |
... |
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)
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