pomp_examples {pomp} | R Documentation |
pre-built pomp examples
Description
Examples of pomp objects containing models and data.
Details
pomp includes a number of pre-built examples of pomp objects and data that can be analyzed using pomp methods. These include:
blowflies
Data from Nicholson's experiments with sheep blowfly populations
blowflies1()
A pomp object with some of the blowfly data together with a discrete delay equation model.
blowflies2()
A variant of
blowflies1
.bsflu
Data from an outbreak of influenza in a boarding school.
dacca()
Fifty years of census and cholera mortality data, together with a stochastic differential equation transmission model (King et al. 2008).
ebolaModel()
Data from the 2014 West Africa outbreak of Ebola virus disease, together with simple transmission models (King et al. 2015).
gompertz()
The Gompertz population dynamics model, with simulated data.
LondonYorke
Data on incidence of several childhood diseases (London and Yorke 1973)
ewmeas
Measles incidence data from England and Wales
ewcitmeas
Measles incidence data from 7 English cities
ou2()
A 2-D Ornstein-Uhlenbeck process with simulated data
parus
Population censuses of a Parus major population in Wytham Wood, England.
ricker
The Ricker population dynamics model, with simulated data
rw2
A 2-D Brownian motion model, with simulated data.
sir()
A simple continuous-time Markov chain SIR model, coded using Euler-multinomial steps, with simulated data.
sir2()
A simple continuous-time Markov chain SIR model, coded using Gillespie's algorithm, with simulated data.
verhulst()
The Verhulst-Pearl (logistic) model, a continuous-time model of population dynamics, with simulated data
See also the tutorials on the package website for more examples.
References
Anonymous. Influenza in a boarding school. British Medical Journal 1, 587, 1978.
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.
A.A. King, M. Domenech de Cellès, F.M.G. Magpantay, and P. Rohani. Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola. Proceedings of the Royal Society of London, Series B 282, 20150347, 2015. doi:10.1098/rspb.2015.0347.
W. P. London and J. A. Yorke, Recurrent outbreaks of measles, chickenpox and mumps: I. Seasonal variation in contact rates. American Journal of Epidemiology 98, 453–468, 1973. doi:10.1093/oxfordjournals.aje.a121575.
A.J. Nicholson. The self-adjustment of populations to change. Cold Spring Harbor Symposia on Quantitative Biology 22, 153–173, 1957. doi:10.1101/SQB.1957.022.01.017.
See Also
More examples provided with pomp:
blowflies
,
childhood_disease_data
,
compartmental_models
,
dacca()
,
ebola
,
gompertz()
,
ou2()
,
ricker()
,
rw2()
,
verhulst()