Transport through soil water — mec

Simulates the spread of Phytophthora cinnamomi inoculum within the soil matrix through the soil water

Usage

mec_soilwater(dem, poi, th = 100, quiet = FALSE)

Arguments

dem: A single-band SpatRaster with a digital elevation model
poi: A single-point sf object denoting the point of interest to run the simulations
th: Threshold of flow accumulation to delineate streams
quiet: A logical value. If TRUE, suppresses any informational messages. Defaults to FALSE.

Value

A SpatRaster

Details

This function models inoculum movement in soil, considering flow direction and altitude under wet and intermediate moisture conditions. It identifies pixels where flow direction matches or is adjacent to the foci, then processes connected pixels based on altitude differences. The result is a binary raster showing the spatial pattern of inoculum dispersal, constrained by topography and moisture.

References

Ristaino, J., Gumpertz, M., 2000. New Frontiers in the Study of Dispersal and Spatial Analysis of Epidemics Caused by Species in the Genus Phytophthora. Annu. Rev. Phytopathol. 38, 541–576. doi:10.1146/annurev.phyto.38.1.541

Vannini, A., Natili, G., Anselmi, N., Montaghi, A., Vettraino, A.M., 2010. Distribution and gradient analysis of Ink disease in chestnut forests. For. Pathol. 40, 73–86. doi:10.1111/j.1439-0329.2009.00609.x

Vannini, A., Natili, G., Thomidis, T., Belli, C., Morales-Rodriguez, C., 2021. Anthropogenic and landscape features are associated with ink disease impact in Central Italy. For. Pathol. 51, e12722. doi:10.1111/efp.12722

Examples

## load packages
library(phytorisk)
library(sf)
library(terra)

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

## simulate mechanism
mec_soilwater_sr <- mec_soilwater(dem_sr, poi_sf)
#> Loading required namespace: flowdem
#> ℹ Filling DEM...
#> ✔ DEM filled [75ms]
#> 
#> ℹ Filling basins...
#> ✔ Basins filled [26ms]
#> 
#> ℹ Removing depressions...
#> ✔ Depressions removed [25ms]
#> 
#> ℹ Filling depressions...
#> ✔ Depressions filled [38ms]
#> 
#> ℹ Getting flow directions...
#> ✔ Flow directions [32ms]
#> 
#> ℹ Calculating flow accumulation...
#> ✔ Flow accumulation calculated [30ms]
#> 
#> ℹ Delineating streams...
#> ✔ Streams delineated [26ms]
#> 
#> ℹ Determining the wet front
#> ✔ Wet front determined [932ms]
#>