Calculate structural connectivity
Source:R/lsm_connectivity_strutural.R
lsm_connectivity_structural.RdIdentifies patch and calculates area in hectare.
Usage
lsm_connectivity_structural(
input,
output = NULL,
zero_as_null = FALSE,
id_direction = 8,
area_round_digit = 0,
area_unit = "ha",
map_connec_struct = TRUE,
map_connec_struct_area = FALSE,
nprocs = 1,
memory = 300
)Arguments
- input
[character]Habitat map (binary classification: e.g., 1/0 or 1/NA) in GRASS.- output
[character]Output map base name in GRASS.- zero_as_null
[logical]If TRUE, non-habitat (0) cells are converted to NULL.- id_direction
[numeric]Neighborhood for clumping (4 or 8).- area_round_digit
[integer]Decimal digits for area rounding.- area_unit
[character]Area unit:"ha","m2", or"km2".- map_id
[logical]Keep fragment ID raster?- map_ncell
[logical]Output raster with fragment cell counts?- map_area
[logical]Output raster with fragment area?
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)
# structural connectivity
lsmetrics::lsm_connectivity_structural(input = "r",
zero_as_null = FALSE,
map_connec_struct = TRUE,
map_connec_struct_area = TRUE)
#> Error in lsmetrics::lsm_connectivity_structural(input = "r", zero_as_null = FALSE, map_connec_struct = TRUE, map_connec_struct_area = TRUE): object 'region_input' not found
# files
rgrass::execGRASS(cmd = "g.list", type = "raster")
#> r
# import from grass to r
r_struct_connec_area <- rgrass::read_RAST("r_struct_connec_area", flags = "quiet", return_format = "terra")
#> Error in sanitize_layername(name = vname[i], type = "raster", mapsets = msp, ignore.stderr = ignore.stderr): r_struct_connec_area not found in mapsets in search path: PERMANENT
plot(r_struct_connec_area, legend = FALSE, axes = FALSE, main = "Structural connected area (ha)")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'r_struct_connec_area' not found
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r_struct_connec_area)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'text': object 'r_struct_connec_area' not found
# import from grass to r
r_struct_connec <- rgrass::read_RAST("r_struct_connec", flags = "quiet", return_format = "terra")
#> Error in sanitize_layername(name = vname[i], type = "raster", mapsets = msp, ignore.stderr = ignore.stderr): r_struct_connec not found in mapsets in search path: PERMANENT
plot(r_struct_connec, legend = FALSE, axes = FALSE, main = "Structural connectivity (ha)")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'r_struct_connec' not found
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r_struct_connec)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'text': object 'r_struct_connec' not found
# delete grassdb
unlink("grassdb", recursive = TRUE)