dacca function

Model of cholera transmission for historic Bengal.

dacca constructs a pomp object containing census and cholera mortality data from the Dacca district of the former British province of Bengal over the years 1891 to 1940 together with a stochastic differential equation transmission model. The model is that of King et al. (2008). The parameters are the MLE for the SIRS model with seasonal reservoir. data

dacca(
  gamma = 20.8,
  eps = 19.1,
  rho = 0,
  delta = 0.02,
  deltaI = 0.06,
  clin = 1,
  alpha = 1,
  beta_trend = -0.00498,
  logbeta = c(0.747, 6.38, -3.44, 4.23, 3.33, 4.55),
  logomega = log(c(0.184, 0.0786, 0.0584, 0.00917, 0.000208, 0.0124)),
  sd_beta = 3.13,
  tau = 0.23,
  S_0 = 0.621,
  I_0 = 0.378,
  Y_0 = 0,
  R1_0 = 0.000843,
  R2_0 = 0.000972,
  R3_0 = 1.16e-07
)

Arguments

• gamma: recovery rate
• eps: rate of waning of immunity for severe infections
• rho: rate of waning of immunity for inapparent infections
• delta: baseline mortality rate
• deltaI: cholera mortality rate
• clin: fraction of infections that lead to severe infection
• alpha: transmission function exponent
• beta_trend: slope of secular trend in transmission
• logbeta: seasonal transmission rates
• logomega: seasonal environmental reservoir parameters
• sd_beta: environmental noise intensity
• tau: measurement error s.d.
• S_0: initial susceptible fraction
• I_0: initial fraction of population infected
• Y_0: initial fraction of the population in the Y class
• R1_0, R2_0, R3_0: initial fractions in the respective R classes

Returns

dacca returns a pomp object containing the model, data, and MLE parameters, as estimated by King et al. (2008).

Details

Data are provided courtesy of Dr. Menno J. Bouma, London School of Tropical Medicine and Hygiene.

Examples

# takes too long for R CMD check
  po <- dacca()
  plot(po)
  ## MLE:
  coef(po)
  plot(simulate(po))

References

A.A. King, E.L. Ionides, M. Pascual, and M.J. Bouma. Inapparent infections and cholera dynamics. Nature 454 , 877-880, 2008. tools:::Rd_expr_doi("10.1038/nature07084") .

See Also

More examples provided with pomp: blowflies, childhood_disease_data, compartmental_models, ebola, gompertz(), ou2(), pomp_examples, ricker(), rw2(), verhulst()

More data sets provided with pomp: blowflies, bsflu, childhood_disease_data, ebola, parus