dacca {pomp} | R Documentation |
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
A.A. King, E.L. Ionides, M. Pascual, and M.J. Bouma. Inapparent infections and cholera dynamics. Nature 454, 877-880, 2008. 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
Examples
# takes too long for R CMD check
po <- dacca()
plot(po)
## MLE:
coef(po)
plot(simulate(po))