| panelMeasles {panelPomp} | R Documentation |
Make a panelPomp model using UK measles data.
Description
The model is a modified panelPomp version of the model of He et al. 2010. The model is a stochastic SEIR model that accounts for population demographics in the form of births and deaths. Because of the increased transmission that results from school-aged children entering the susceptible pool once they begin attending classes for the first time, the model includes a birth-cohort effect, which moves a specified faction of the cohort into the susceptible pool all at once. The model also includes a seasonality in transmission rate that is larger during school terms thn it is during holidays.
Usage
panelMeasles(
units = c("Bedwellty", "Birmingham", "Bradford", "Bristol", "Cardiff", "Consett",
"Dalton.in.Furness", "Halesworth", "Hastings", "Hull", "Leeds", "Lees", "Liverpool",
"London", "Manchester", "Mold", "Northwich", "Nottingham", "Oswestry", "Sheffield"),
starting_pparams = NULL,
interp_method = c("shifted_splines", "linear"),
first_year = 1950,
last_year = 1963,
dt = 1/365.25
)
Arguments
units |
Character vector of units in uk_measles to be used in the panel model. |
starting_pparams |
Parameters in the list format, having shared and specific components. Set to NULL to assign NA values. |
interp_method |
Method used to interpolate population and births.
Possible options are |
first_year |
Integer for the first full year of data desired. |
last_year |
Integer for the last full year of data desired. |
dt |
Size of the time step. |
Value
A panelPomp object.
References
D. He, E.L. Ionides, and A.A. King. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. Journal of the Royal Society Interface 7, 271–283, 2010.
See Also
Other panelPomp examples:
contacts(),
panelGompertz(),
panelRandomWalk()
Examples
panelMeasles(units = "London")