Dispersion by animals — mec_zoospread • phytorisk

Optional Module. Simulates dispersion by domestic and wild animal movement

Usage

mec_zoospread(
  aoi,
  poi,
  mec_surfacewater,
  n_animals = 5,
  n_steps = 100,
  pixel_size = 1,
  n_iter = 10,
  dist = 5,
  quiet = FALSE
)

Arguments

aoi: A sf polygon representing the area of interest. Used to mask the tree cover
poi: A single-point sf object denoting the point of interest to run the simulations
mec_surfacewater: The result of mec_surfacewater
n_animals: Number of simulated animals
n_steps: Number of steps of each animal for the simulations
pixel_size: Size of the movement in pixels
n_iter: Number of random iterations for each animal
dist: Filter trajectories less than the specified meters away of the POI (susceptible to inoculum)
quiet: A logical value. If TRUE, suppresses any informational messages. Defaults to FALSE.

Value

A SpatRaster

Details

This function models animal movement as a series of straight-line steps towards resource sources, while avoiding exclusion areas and staying within defined boundaries. It randomly assigns initial animal positions and calculates movement direction towards resources. The direction is normalized and randomized using a rotation matrix. Animal trajectories are stored in vector format, and those crossing the foci are identified for further analysis. Simulation parameters, such as the number of animals and steps, are set at the start.

References

Kliejunas, J.T., Ko, W.H., 1976. Dispersal of Phytophthora cinnamomi on the island of Hawaii. Phytopathology 66, 457–460.

Li, A.Y., Williams, N., Fenwick, S.G., Hardy, G.E.St.J., Adams, P.J., 2014b. Potential for dissemination of Phytophthora cinnamomi by feral pigs via ingestion of infected plant material. Biol. Invasions 16, 765–774. doi:10.1007/s10530-013-0535-7

Cardillo, E., Acedo, A., Abad, E., 2018. Topographic effects on dispersal patterns of Phytophthora cinnamomi at a stand scale in a Spanish heathland. PloS One 13, e0195060.

Examples

# \donttest{
## load packages
library(phytorisk)
library(sf)
library(terra)

## load data
poi_sf <- st_read(
  system.file("spatial/poi.geojson", package = "phytorisk"),
  quiet = TRUE
)
dem_sr <- rast(system.file("spatial/dem_light.tiff", package = "phytorisk"))
trees_sr <- rast(system.file("spatial/trees_light.tiff", package = "phytorisk"))
aoi_sf <- st_read(
  system.file("spatial/tejera.geojson", package = "phytorisk"),
  quiet = TRUE
)

## first, calculate the soil water and surface water dispersal mechanisms
mec_soilwater_sr <- mec_soilwater(dem_sr, poi_sf)
#> ℹ Filling DEM...
#> ✔ DEM filled [25ms]
#> 
#> ℹ Filling basins...
#> ✔ Basins filled [25ms]
#> 
#> ℹ Removing depressions...
#> ✔ Depressions removed [18ms]
#> 
#> ℹ Filling depressions...
#> ✔ Depressions filled [19ms]
#> 
#> ℹ Getting flow directions...
#> ✔ Flow directions [32ms]
#> 
#> ℹ Calculating flow accumulation...
#> ✔ Flow accumulation calculated [30ms]
#> 
#> ℹ Delineating streams...
#> ✔ Streams delineated [34ms]
#> 
#> ℹ Determining the wet front
#> ✔ Wet front determined [732ms]
#> 
mec_surface_sr   <- mec_surfacewater(dem_sr, mec_soilwater_sr, poi_sf)
#> ℹ Calculating natural drainage network...
#> ✔ Natural drainage network calculated [69ms]
#> 
#> ℹ Identifying surface water close to foci...
#> ✔ Surface water close to foci identified [96ms]
#> 
#> ℹ Finding connected pixels...
#> ✔ Finished [843ms]
#> 

## calculate the spread by animals (dummy example)
mec_zoospread_sr <- mec_zoospread(
  aoi = aoi_sf,
  poi = poi_sf,
  mec_surface = mec_surface_sr,
  n_animals = 5,
  n_steps = 5,
  pixel_size = 1,
  n_iter = 2,
  dist = 5
)
#> 
#> ── Starting animal movement simulation ──
#> 
#> ✔ Simulation completed. 2 trajectories generated.
#> ℹ Preparing results
#> ! There are no trajectories within 5 meters of the inoculum
#> ℹ Preparing results

#> ✔ Success [26ms]
#> 
# }