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r.grow

Source: R/lsm_aux_grow.R
lsm_aux_grow.Rd

Fast replacement for r.grow using r.grow.distance

Usage

lsm_aux_grow(
  input,
  output,
  flags = NULL,
  radius = 1.01,
  metric = "euclidean",
  old = "",
  new = "",
  mapunits = FALSE
)

Arguments

input

[character=""]
Habitat map, following a binary classification (e.g. values 1,0 or 1,NA for habitat,non-habitat) inside GRASS Data Base.

output

[character=""]
Map name output inside GRASS Data Base.

flags

[character=""]

radius

[logical(1)=FALSE]
If TRUE, the function treats non-habitat cells as null; if FALSE, the function converts non-habitat zero cells to null cells.

metric

[numeric()]

old

[numeric()]

new

[numeric()]

mapunits

[numeric()]

Details

AUTHOR(S): Glynn Clements PURPOSE: Fast replacement for r.grow using r.grow.distance

COPYRIGHT: (C) 2008 by Glynn Clements

This program is free software under the GNU General Public License (>=v2). Read the file COPYING that comes with GRASS for details.

Examples

library(lsmetrics)
library(terra)

# read habitat data
r <- lsmetrics::lsm_toy_landscape(proj_type = "meters")

# plot
plot(r, legend = FALSE, axes = FALSE, main = "Binary habitat")
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r)


# find grass
path_grass <- system("grass --config path", inter = TRUE) # windows users need to find the grass gis path installation, e.g. "C:/Program Files/GRASS GIS 8.3"

# create grassdb
rgrass::initGRASS(gisBase = path_grass,
                  SG = r,
                  gisDbase = "grassdb",
                  location = "newLocation",
                  mapset = "PERMANENT",
                  override = TRUE)
#> gisdbase    grassdb 
#> location    newLocation 
#> mapset      PERMANENT 
#> rows        16 
#> columns     16 
#> north       7525600 
#> south       7524000 
#> west        234000 
#> east        235600 
#> nsres       100 
#> ewres       100 
#> projection:
#>  PROJCRS["WGS 84 / UTM zone 23S",
#>     BASEGEOGCRS["WGS 84",
#>         ENSEMBLE["World Geodetic System 1984 ensemble",
#>             MEMBER["World Geodetic System 1984 (Transit)"],
#>             MEMBER["World Geodetic System 1984 (G730)"],
#>             MEMBER["World Geodetic System 1984 (G873)"],
#>             MEMBER["World Geodetic System 1984 (G1150)"],
#>             MEMBER["World Geodetic System 1984 (G1674)"],
#>             MEMBER["World Geodetic System 1984 (G1762)"],
#>             MEMBER["World Geodetic System 1984 (G2139)"],
#>             ELLIPSOID["WGS 84",6378137,298.257223563,
#>                 LENGTHUNIT["metre",1]],
#>             ENSEMBLEACCURACY[2.0]],
#>         PRIMEM["Greenwich",0,
#>             ANGLEUNIT["degree",0.0174532925199433]],
#>         ID["EPSG",4326]],
#>     CONVERSION["UTM zone 23S",
#>         METHOD["Transverse Mercator",
#>             ID["EPSG",9807]],
#>         PARAMETER["Latitude of natural origin",0,
#>             ANGLEUNIT["degree",0.0174532925199433],
#>             ID["EPSG",8801]],
#>         PARAMETER["Longitude of natural origin",-45,
#>             ANGLEUNIT["degree",0.0174532925199433],
#>             ID["EPSG",8802]],
#>         PARAMETER["Scale factor at natural origin",0.9996,
#>             SCALEUNIT["unity",1],
#>             ID["EPSG",8805]],
#>         PARAMETER["False easting",500000,
#>             LENGTHUNIT["metre",1],
#>             ID["EPSG",8806]],
#>         PARAMETER["False northing",10000000,
#>             LENGTHUNIT["metre",1],
#>             ID["EPSG",8807]]],
#>     CS[Cartesian,2],
#>         AXIS["(E)",east,
#>             ORDER[1],
#>             LENGTHUNIT["metre",1]],
#>         AXIS["(N)",north,
#>             ORDER[2],
#>             LENGTHUNIT["metre",1]],
#>     USAGE[
#>         SCOPE["Navigation and medium accuracy spatial referencing."],
#>         AREA["Between 48°W and 42°W, southern hemisphere between 80°S and equator, onshore and offshore. Brazil."],
#>         BBOX[-80,-48,0,-42]],
#>     ID["EPSG",32723]] 

# import raster from r to grass
rgrass::write_RAST(x = r, flags = c("o", "overwrite", "quiet"), vname = "r", verbose = FALSE)

# clump
rgrass::execGRASS(cmd = "r.mapcalc", expression = "r_null = if(r == 1, 1, null())")
rgrass::execGRASS(cmd = "r.clump", flags = c("d", "overwrite"), input = "r_null", output = "r_id")
#> Pass 1 of 2...
#>    0%   6%  12%  18%  25%  31%  37%  43%  50%  56%  62%  68%  75%  81%  87%  93% 100%
#> Generating renumbering scheme...
#>    0%  14%  28%  42%  57%  71%  85% 100%
#> Pass 2 of 2...
#>    0%   6%  12%  18%  25%  31%  37%  43%  50%  56%  62%  68%  75%  81%  87%  93% 100%
#> r.clump complete. 6 clumps.

# grow
lsmetrics::lsm_aux_grow(input = "r_id", output = "r_id_grow")
#> Reading raster map <r_id>...
#>    0%   6%  12%  18%  25%  31%  37%  43%  50%  56%  62%  68%  75%  81%  87%  93% 100%
#> Writing output raster maps...
#>    0%   6%  12%  18%  25%  31%  37%  43%  50%  56%  62%  68%  75%  81%  87%  93% 100%
#> Color table for raster map <r_id_grow> set to 'r_id'

# files
rgrass::execGRASS(cmd = "g.list", type = "raster")
#> r
#> r_id
#> r_id_grow
#> r_null

# import from grass to r
r_id <- rgrass::read_RAST("r_id", flags = "quiet", return_format = "terra")

# plot
plot(r_id, legend = FALSE, axes = FALSE, main = "Fragment id")
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r_id)


# import from grass to r
r_id_grow <- rgrass::read_RAST("r_id_grow", flags = "quiet", return_format = "terra")

plot(r_id_grow, legend = FALSE, axes = FALSE, main = "Fragment grow")
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r_id_grow)


# delete grassdb
unlink("grassdb", recursive = TRUE)