Identifies landscape morphological — lsm

Identifies landscape morphological: matrix, core, edge, corridor, stepping stone, branch, and perforation

Usage

lsm_morphology(
  input,
  output = NULL,
  zero_as_null = FALSE,
  region_input = FALSE,
  morphology = "all",
  table_morphology = FALSE,
  area_round_digit = 0,
  area_unit = "ha",
  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) inside GRASS Data Base.
output: [character=""]
Map name output inside GRASS Data Base.
morphology: [character=""]
nprocs: [numeric()]
memory: [numeric()]
zero_as_na: [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.

Examples

library(lsmetrics)
library(terra)

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

# 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       -22.35558 
#> south       -22.36995 
#> west        -47.58312 
#> east        -47.56875 
#> nsres       0.000898125 
#> ewres       0.000898125 
#> projection:
#>  GEOGCRS["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]],
#>     CS[ellipsoidal,2],
#>         AXIS["geodetic latitude (Lat)",north,
#>             ORDER[1],
#>             ANGLEUNIT["degree",0.0174532925199433]],
#>         AXIS["geodetic longitude (Lon)",east,
#>             ORDER[2],
#>             ANGLEUNIT["degree",0.0174532925199433]],
#>     USAGE[
#>         SCOPE["Horizontal component of 3D system."],
#>         AREA["World."],
#>         BBOX[-90,-180,90,180]],
#>     ID["EPSG",4326]] 

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

# morphology
lsmetrics::lsm_morphology(input = "r", table_morphology = TRUE)
#> Converting zero as null
#> Identifying fragments
#> Identifying matrix
#> Identifying core
#> Identifying stepping stone
#> Identifying edge
#> Converting zero as null
#> Identifying fragments
#> Creating matrix
#> Filling holes
#> Cleaning data
#> WARNING: Raster map <r_morphology_binary_aux_fill_hole_matrix_id@PERMANENT>
#>          is a base map for
#>          <r_morphology_binary_aux_fill_hole_matrix_id_fill@PERMANENT>.
#>          Remove forced.
#> Identifying branch, corridor and perforation
#> Color table for raster map <r_morphology_branch_corridor_id_dila> set to
#> 'r_morphology_branch_corridor_id'
#> Identifying perforation
#> Identifying corridor
#> Identifying branch
#> Changing raster color
#> Table exporting
#> Cleaning data

# files
rgrass::execGRASS(cmd = "g.list", type = "raster")
#> r
#> r_morphology
#> r_morphology_branch
#> r_morphology_core
#> r_morphology_corridor
#> r_morphology_edge
#> r_morphology_matrix
#> r_morphology_perforation
#> r_morphology_stepping_stone

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

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


# table
table_morphology <- readr::read_csv("r_table_morphology.csv", show_col_types = FALSE)
table_morphology
#> # A tibble: 7 × 4
#>   morphology     morphology_id  area ncell
#>   <chr>                  <dbl> <dbl> <dbl>
#> 1 matrix                     0   134   146
#> 2 core                       1    22    24
#> 3 edge                       2    51    55
#> 4 corridor                   3     3     3
#> 5 branch                     4     6     6
#> 6 stepping_stone             5     3     3
#> 7 perforation                6    17    19

# delete grassdb
unlink("r_table_morphology.csv")
unlink("grassdb", recursive = TRUE)