Create a SpatRaster of SVEIRD model compartment raster data — getSVEIRD.SpatRaster • spatialEpisim.foundation

Create a SpatRaster objects, with a layer for each component in an SVEIRD epidemic model.

Usage

getSVEIRD.SpatRaster(subregions, population, aggregationFactor = NULL)

Arguments

subregions: a SpatVector object of subregions used to crop the population SpatRaster before creating the other layers in the raster object to represent the other compartments in a SVEIRD epidemic model. If it is missing no cropping is performed.
population: a SpatRaster of population count data; it must be pre-aggregated if any aggregation is to be used during the simulation; none is performed by this function or downstream functions in the overall implementation of SVEIRD.BayesianDataAssimilation simulations.
aggregationFactor: the number of cells in any direction to aggregate together into one, in the input raster, after masking with the subregions vector.

Value

a SpatRaster, with layers for the SVERID components

Details

The SpatRaster objects for the VEIRD components are empty, the input SpatRaster is taken as the Suscptible layer, the only layer with non-zero values (if any existed before).

Author

Bryce Carson

Michael Myer

Ashok Krishnmaurthy

Examples

subregionsSpatVector <- terra::vect(
  system.file(
    "extdata",
    ## COD: Nord-Kivu and Ituri (Democratic Republic of Congo)
    "subregionsSpatVector",
    package = "spatialEpisim.foundation",
    mustWork = TRUE
  )
)
susceptibleSpatRaster <- terra::rast(
  system.file(
    "extdata",
    "susceptibleSpatRaster.tif", # Congo population
    package = "spatialEpisim.foundation",
    mustWork = TRUE
  )
)
getSVEIRD.SpatRaster(subregionsSpatVector, susceptibleSpatRaster,
                     aggregationFactor = 10)
#> class       : SpatRaster 
#> dimensions  : 69, 49, 6  (nrow, ncol, nlyr)
#> resolution  : 0.08333333, 0.08333333  (x, y)
#> extent      : 27.22375, 31.30708, -2.075416, 3.674584  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> names       : Susceptible, Vaccinated, Exposed, Infected, Recovered, Dead 
#> min values  :           0,          0,       0,        0,         0,    0 
#> max values  :      739582,          0,       0,        0,         0,    0 

## Omitting the aggregation factor argument will prevent aggregation. An
## aggregation factor of zero or one is meaningless and will produce an
## error.
getSVEIRD.SpatRaster(subregionsSpatVector, susceptibleSpatRaster)
#> class       : SpatRaster 
#> dimensions  : 689, 487, 6  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 27.22375, 31.28208, -2.067083, 3.674584  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> varnames    : susceptibleSpatRaster 
#>               susceptibleSpatRaster 
#> names       : Susceptible, Vaccinated, Exposed, Infected, Recovered, Dead 
#> min values  :        0.00,          0,       0,        0,         0,    0 
#> max values  :    32905.59,          0,       0,        0,         0,    0 

## Omitting a SpatVector will return a SpatRaster with layers representing each
## of SVEIRD without cropping or masking the input SpatRaster in any way.
getSVEIRD.SpatRaster(subregionsSpatVector, susceptibleSpatRaster)
#> class       : SpatRaster 
#> dimensions  : 689, 487, 6  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 27.22375, 31.28208, -2.067083, 3.674584  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> varnames    : susceptibleSpatRaster 
#>               susceptibleSpatRaster 
#> names       : Susceptible, Vaccinated, Exposed, Infected, Recovered, Dead 
#> min values  :        0.00,          0,       0,        0,         0,    0 
#> max values  :    32905.59,          0,       0,        0,         0,    0