SepTest (version 0.0.1)

run_fmd_example: Spatio-temporal analysis of the 2001 FMD outbreak (illustrative example)

Description

This function tests first-order separability for the foot-and-mouth disease (FMD) outbreak data observed at the North Cumbria study region provided by the stpp package.

Usage

run_fmd_example()

Value

An object of class "test" returned by dHS.test.

Details

The example includes kernel-based estimates of the spatio-temporal intensity and related separability diagnostics on a regular spatio-temporal grid for fmd data as well as the dHSIC test.

The datasets fmd and northcumbria are loaded from the stpp package and are used purely for illustration. They do not contain confidential information and have no scientific value.

References

Diggle, P., Rowlingson, B. and Su, T. (2005). Point process methodology for on-line spatio-temporal disease surveillance. Environmetrics, 16, 423--434.

See Also

fmd, northcumbria, S.based.functions, dHS.test

Examples

# \donttest{
if (requireNamespace("stpp", quietly = TRUE) ) {

  library(stpp)

  # Load data
  data("fmd", "northcumbria", package = "stpp")

  # Define spatial and temporal region
  s.region <- northcumbria / 1000
  t.region <- c(0, 200)

  # Create a spatio-temporal point pattern
  X <- as.3dpoints(
    fmd[, 1] / 1000,
    fmd[, 2] / 1000,
    fmd[, 3]
  )

  # Define observation window
  ObsW <- spatstat.geom::owin(
    poly = list(
      x = s.region[, 1],
      y = s.region[, 2]
    )
  )

  # Run Hilbert-Schmidt independence test
  oldpar <- par(no.readonly = TRUE)  # save current graphics settings
  on.exit(par(oldpar), add = TRUE)   # restore after example

  dHS.test(
    X,
    sim.procedure = "block_per",
    nblocks = 5L,
    nperm = 1999L,
    nsim = 199L,
    bandwidth = NULL
  )
 }
# }