incubsim {EpiLPS} | R Documentation |
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).
incubsim(incubdist = c("LogNormal","Weibull","MixWeibull", "Gamma"), coarseness = 1,
n = 100, tmax = 20, tgridlen = 500, plotsim = FALSE)
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? |
A list including (among others) the left and right bounds of the incubation period.
Oswaldo Gressani oswaldo_gressani@hotmail.fr
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.
simdat <- incubsim(n = 50) # Simulation of incubation times for 50 cases.
simdat$Dobsincub # Left and right bounds of incubation period.