sir: Compartmental epidemiological models

In pomp: Statistical Inference for Partially Observed Markov Processes

Description

euler.sir is a pomp object encoding a simple seasonal SIR model. Simulation is performed using an Euler multinomial approximation. gillespie.sir has the same model implemented using Gillespie's algorithm. bbs is a nonseasonal SIR model together with data from a 1978 outbreak of influenza in a British boarding school.

Details

This and similar examples are discussed and constructed in tutorials available on the package website.

The boarding school influenza outbreak is described in Anonymous (1978).

References

Anonymous (1978). Influenza in a boarding school. British Medical Journal 1:587

See Also

pomp and the tutorials on the package website.

Examples

pompExample(euler.sir)
plot(euler.sir)
plot(simulate(euler.sir,seed=20348585))
coef(euler.sir)

pompExample(gillespie.sir)
plot(gillespie.sir)
plot(simulate(gillespie.sir,seed=20348585))
coef(gillespie.sir)

pompExample(bbs)
plot(bbs)
coef(bbs)

Example output

In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nbasis','degree','period'
newly created object(s):
 euler.sir 
   gamma       mu     iota    beta1    beta2    beta3  beta.sd      pop 
2.60e+01 2.00e-02 1.00e-02 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06 
     rho      S_0      I_0      R_0 
6.00e-01 6.50e-02 1.00e-03 9.35e-01 
In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
newly created object(s):
 gillespie.sir 
       gamma           mu         iota        beta1        beta2        beta3 
2.400000e+01 1.428571e-02 1.000000e-01 3.300000e+02 4.100000e+02 4.900000e+02 
         rho          S_0          I_0          R_0          pop      beta.sd 
1.000000e-01 5.000000e-02 1.000000e-04 9.500000e-01 1.000000e+06 0.000000e+00 
In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nbasis','degree','period','logvar','logitvar'
newly created object(s):
 bbs 
       gamma           mu         iota         beta      beta.sd          pop 
   0.3333333    0.0000000    0.0000000    1.4000000    0.0000000 1400.0000000 
         rho        sigma          S_0          I_0          R_0 
   0.9000000    3.6000000    0.9990000    0.0010000    0.0000000 

pomp documentation built on May 2, 2019, 4:09 p.m.