Calculate landscape diversity using r.diversity module.
Usage
lsm_diversity_parallel(
input,
output = NULL,
buffer_radius,
index,
alpha = NULL,
grid_size,
grid_delete = FALSE,
nprocs = 1,
memory = 300
)Arguments
- input
[character=""]
Habitat map, following a binary classification (e.g. values 1,0 or 1,NA for habitat,non-habitat).- output
[character=""]
Habitat map output name inside GRASS Data Base.- buffer_radius
[numeric()]
Integer indicating window size.- index
[character=""]
Integer indicating window size.- grid_size
[numeric()]
Integer indicating window size.- grid_delete
[numeric()]
Integer indicating window size.- nprocs
[numeric()]- memory
[numeric()]
Examples
library(lsmetrics)
library(terra)
# read habitat data
r <- lsmetrics::lsm_toy_landscape(type = "class")
# plot
plot(r, legend = FALSE, axes = FALSE, main = "Classes")
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(as.polygons(r), add = TRUE)
text(r)
#> Warning: [readValues] raster has no values
#> Warning: [as.points] raster has no values
#> Error in text.default(xy[, 1], xy[, 2], labels, ...): zero-length 'labels' specified
# 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["unknown",
#> BASEGEOGCRS["unknown",
#> DATUM["World Geodetic System 1984",
#> ELLIPSOID["WGS 84",6378137,298.257223563,
#> LENGTHUNIT["metre",1]],
#> ID["EPSG",6326]],
#> PRIMEM["Greenwich",0,
#> ANGLEUNIT["degree",0.0174532925199433],
#> ID["EPSG",8901]]],
#> 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]],
#> ID["EPSG",17023]],
#> CS[Cartesian,2],
#> AXIS["(E)",east,
#> ORDER[1],
#> LENGTHUNIT["metre",1,
#> ID["EPSG",9001]]],
#> AXIS["(N)",north,
#> ORDER[2],
#> LENGTHUNIT["metre",1,
#> ID["EPSG",9001]]]]
# import raster from r to grass
rgrass::write_RAST(x = r, flags = c("o", "overwrite"), vname = "r")
#> Error: [writeRaster] there are no cell values
# diversity
lsmetrics::lsm_diversity_parallel(input = "r", index = "shannon", buffer_radius = 100, grid_size = 1000, grid_delete = FALSE, nprocs = 5, memory = 1e5)
#> Error in rgrass::execGRASS(cmd = "g.region", flags = "a", raster = input, res = as.character(grid_size)): The command:
#> g.region -a raster=r res=1000
#> produced an error (1) during execution:
#> ERROR: Raster map <r> not found
# files
# rgrass::execGRASS(cmd = "g.list", type = "vector")
# rgrass::execGRASS(cmd = "g.list", type = "raster")
# import from grass to r
v <- rgrass::read_VECT("grid", flags = "quiet")
#> Error in execGRASS("v.info", flags = "t", map = vname, layer = layer, intern = TRUE, ignore.stderr = ignore.stderr): The command:
#> v.info -t map=grid layer=1
#> produced an error (1) during execution:
#> ERROR: Vector map <grid> not found
r_div_buf100 <- rgrass::read_RAST("r_diversity_shannon_buffer100", flags = "quiet", return_format = "terra")
#> Error in sanitize_layername(name = vname[i], type = "raster", mapsets = msp, ignore.stderr = ignore.stderr): r_diversity_shannon_buffer100 not found in mapsets in search path: PERMANENT
# plot
plot(r_div_buf100, legend = FALSE, axes = FALSE, main = "Landscape diversity (Shannon) (buffer 100 m)")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'r_div_buf100' not found
plot(as.polygons(r, dissolve = FALSE), lwd = .1, add = TRUE)
plot(v, lwd = 3, border = "blue", add = TRUE)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'v' not found
text(v, cex = 3, col = "blue")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'text': object 'v' not found
text(r_div_buf100, digits = 1, cex = .75)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'text': object 'r_div_buf100' not found
# delete grassdb
unlink("grassdb", recursive = TRUE)