measles2 {spatPomp}

Measles in UK: spatPomp generator with shared or unit-specific parameters

Description

Generate a spatPomp object for measles in the top-U most populous cities in England and Wales. The model is adapted from He et al. (2010) with gravity transport following Park and Ionides (2019). The structure of this spatPomp is designed to accommodate shared and unit-specific parameters. If carrying out spatiotemporal iterated filtering for shared parameters via ibpf, it is necessary to have a unit-specific expansion and so these parameters should be included in expandedParNames. This model and data correspond to the biweekly analysis of Park and Ionides (2020) and Ionides et al (2021). There are small differences with the weekly model and data of He et al (2010) and Ionides, Ning and Wheeler (2022).

Usage

measles2(
  U = 6,
  dt = 2/365,
  N = 391,
  expandedParNames = c("R0", "c", "A", "muIR", "muEI", "sigmaSE", "rho", "psi", "g",
    "S_0", "E_0", "I_0"),
  contractedParNames = NULL,
  simulated = FALSE,
  basic_params = c(alpha = 0.98, iota = 0.1, R0 = 30, c = 0.3, A = 0.5, muIR = 52, muEI =
    52, muD = 0.02, sigmaSE = 0.15, rho = 0.5, psi = 0.15, g = 400, S_0 = 0.032, E_0 =
    5e-05, I_0 = 4e-05)
)

Arguments

U

An integer from 1 to 40 specifying the number of cities to be represented in the spatPomp object.

dt

a numeric (in unit of years) that is used as the Euler time-increment for simulating measles data

N

An integer from 1 to 391 specifying the number of time points.

expandedParNames

specifies parameters that are defined for each unit. This also allows unit perturbations for a parameter with a value shared across units.

contractedParNames

specifies parameters having a shared value across units. Remaining parameters that are neither expanded nor contracted are considered fixed, and will not have a transformation defined for them.

simulated

determines whether to return a simulation from the model or the UK measles data

basic_params

A named vector used to specify shared parameters or unit-specific parameters having common values for each unit.

Value

An object of class ‘spatPomp’ representing a U-dimensional spatially coupled measles POMP model.

References

He, D., Ionides, E. L., and King, A. A. (2010). Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. Journal of the Royal Society Interface, 7(43), 271-283. doi:10.1098/rsif.2009.0151

Park, J. and Ionides, E. L. (2020) Inference on high-dimensional implicit dynamic models using a guided intermediate resampling filter. Statistics and Computing, doi:10.1007/s11222-020-09957-3

Ionides, E. L., Asfaw, K., Park, J., and King, A. A. (2021). Bagged filters for partially observed interacting systems. Journal of the American Statistical Association, doi:10.1080/01621459.2021.1974867

Ionides, E. L., Ning, N., and Wheeler, J. (2022). An iterated block particle filter for inference on coupled dynamic systems with shared and unit-specific parameters. Statistica Sinica, to appear. doi:10.48550/arXiv.2206.03837

Examples

# Complete examples are provided in the package tests
## Not run: 
m <- measles2(U = 5)
# See all the model specifications of the object
spy(m)

## End(Not run)