dacca: Model of cholera transmission for historic Bengal.

In pomp: Statistical Inference for Partially Observed Markov Processes

Model of cholera transmission for historic Bengal.

Description

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.

Usage

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

Details

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

Value

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

References

\King

2008

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

Examples

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

pomp documentation built on Sept. 13, 2024, 1:08 a.m.