Phytophthora ensemble risk — phytorisk

Calculates Phytophthora cinnamomi's ensemble risk from mechanisms

Usage

phytorisk_ensemble(
  mec_soilwater,
  mec_rootcontact,
  mec_surfacewater,
  mec_zoospread = NULL,
  weights = "equal"
)

Arguments

mec_soilwater: The result of mec_soilwater
mec_rootcontact: The result of mec_rootcontact
mec_surfacewater: The result of mec_surfacewater
mec_zoospread: Optional module. The result of mec_zoospread
weights: Weights of the ensemble model. The default uses the same weights for each model. The argument accepts a numeric vector with the corresponding weights. See Details

Value

A SpatRaster

Details

This function calculates the ensemble risk as the weighted sum of the individual risk models as follows:

\(Risk = w_1 \cdot Mec_{soilwater} + w_2 \cdot Mec_{rootcontact} + w_3 \cdot Mec_{mec_surfacewater} + w_4 \cdot Mec_{zoospread}\).

Being \(w_i = 0.25\) when mec_zoospread is not null, and \(w_i = \frac{1}{3}\) when mec_zoospread is null. Additionally, the user can specify a numeric vector of length 3 or 4 specifying the desired weights based on expert criteria.

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 individual mechanisms
mec_soilwater_sr <- mec_soilwater(dem_sr, poi_sf)
#> ℹ Filling DEM...
#> ✔ DEM filled [16ms]
#> 
#> ℹ Filling basins...
#> ✔ Basins filled [22ms]
#> 
#> ℹ Removing depressions...
#> ✔ Depressions removed [15ms]
#> 
#> ℹ Filling depressions...
#> ✔ Depressions filled [16ms]
#> 
#> ℹ Getting flow directions...
#> ✔ Flow directions [16ms]
#> 
#> ℹ Calculating flow accumulation...
#> ✔ Flow accumulation calculated [15ms]
#> 
#> ℹ Delineating streams...
#> ✔ Streams delineated [18ms]
#> 
#> ℹ Determining the wet front
#> ✔ Wet front determined [493ms]
#> 
mec_surface_lst   <- mec_surfacewater(dem_sr, mec_soilwater_sr, poi_sf)
#> ℹ Calculating natural drainage network...
#> ✔ Natural drainage network calculated [35ms]
#> 
#> ℹ Identifying surface water close to foci...
#> ✔ Surface water close to foci identified [36ms]
#> 
#> ℹ Finding connected pixels...
#> ✔ Finished [532ms]
#> 
mec_rootcontact_sr <- mec_rootcontact(trees_sr, aoi_sf, poi_sf)
#> ℹ Preparing tree data...
#> ✔ Tree data prepared [109ms]
#> 
#> ℹ Finding root-to-root contact...
#> ✔ Finished [13.3s]
#> 

## calculate ensemble risk using equal weights
risk_equal_sr <- phytorisk_ensemble(
 mec_soilwater = mec_soilwater_sr,
 mec_rootcontact = mec_rootcontact_sr,
 mec_surfacewater = mec_surface_lst
)

## assign more weight to root-to-root contact
risk_weighted_sr <- phytorisk_ensemble(
 mec_soilwater = mec_soilwater_sr,
 mec_rootcontact = mec_rootcontact_sr,
 mec_surfacewater = mec_surface_lst,
 weights = c(.3, .4, .3)
)
# }