incubsim {EpiLPS} | R Documentation |

## Simulation of incubation times

### Description

This routine simulates symptom onset times, generation times and left and right bounds of infecting exposure windows for source-recipient pairs based on a given incubation distribution and a generation time distribution. The generation time distribution is assumed to be a Weibull with shape 2.826 and scale 5.665 (Ferretti et al. 2020). The incubation distribution can be chosen by the user among:

A LogNormal distribution with a mean of 5.5 days and standard deviation of 2.1 days (Ferretti et al. 2020).

A Weibull distribution (shape-scale parameterization) with a mean of 6.4 days and standard deviation of 2.3 days (Backer et al. 2020).

An artificial bimodal distribution constructed from a mixture of two Weibull distributions.

A Gamma distribution (shape-rate parameterization) with a mean of 3.8 days and standard deviation of 2.9 days (Donnelly et al. 2003).

### Usage

```
incubsim(incubdist = c("LogNormal","Weibull","MixWeibull", "Gamma"), coarseness = 1,
n = 100, tmax = 20, tgridlen = 500, plotsim = FALSE)
```

### Arguments

`incubdist` |
The distribution of the incubation period. |

`coarseness` |
The average coarseness of the data. Default is 1 day. |

`n` |
The sample size. |

`tmax` |
The upper bound on which to evaluate the |

`tgridlen` |
The number of grid points on which to evaluate the density. |

`plotsim` |
Graphical visualization of the simulated data? |

### Value

A list including (among others) the left and right bounds of the incubation period.

### Author(s)

Oswaldo Gressani oswaldo_gressani@hotmail.fr

### References

Ferretti, L., Wymant, C., Kendall, et al. (2020). Quantifying
SARS-CoV-2 transmission suggests epidemic control with digital contact
tracing. *Science*, **368**(6491), eabb6936.

Backer, J. A., Klinkenberg, D., & Wallinga, J. (2020). Incubation
period of 2019 novel coronavirus (2019-nCoV) infections among
travellers from Wuhan, China, 20–28 January 2020. *Eurosurveillance*,
**25**(5), 2000062.

Donnelly, C. A., Ghani, A. C., Leung, G. M., et al. (2003).
Epidemiological determinants of spread of causal agent of severe acute
respiratory syndrome in Hong Kong. *The Lancet*, **361**(9371),
1761-1766.

### Examples

```
simdat <- incubsim(n = 50) # Simulation of incubation times for 50 cases.
simdat$Dobsincub # Left and right bounds of incubation period.
```

*EpiLPS*version 1.3.0 Index]