Description Usage Arguments Author(s) Examples

View source: R/outbreak_step.R

Move forward one generation in the branching process

1 2 3 4 5 6 7 8 9 10 11 12 13 |

`case_data` |
data.table of cases in outbreak so far; initially generated by outbreak_setup |

`disp.iso` |
numeric dispersion parameter for isolated cases (must be >0) |

`disp.com` |
numeric dispersion parameter for non-isolated cases (must be >0) |

`r0isolated` |
numeric reproduction number for isolated cases (must be >0) |

`r0community` |
numeric reproduction number for non-isolated cases (must be >0) |

`incfn` |
function samples from incubation period; generated by dist_setup |

`delayfn` |
function samples from the onset-to-hospitalisation delay; generated by dist_setup |

`prop.ascertain` |
numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1) |

`k` |
numeric skew parameter for sampling the serial interval from the incubation period |

`quarantine` |
logical whether quarantine is in effect, if TRUE then traced contacts are isolated before symptom onset |

Joel Hellewell

1 2 3 4 5 6 7 8 9 10 11 | ```
## Not run:
# incubation period sampling function
incfn <- dist_setup(dist_shape = 2.322737,dist_scale = 6.492272)
# delay distribution sampling function
delayfn <- dist_setup(delay_shape, delay_scale)
# generate initial cases
case_data <- outbreak_setup(num.initial.cases = 5,incfn,delayfn,k=1.95,prop.asym=0)
# generate next generation of cases
case_data <- outbreak_step(case_data,1,0.16,0,2.5,0,incfn,delayfn,0,1.95,FALSE)
## End(Not run)
``` |

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