ebola() R function from [pomp]

Ebola outbreak, West Africa, 2014-2016

Data and models for the 2014--2016 outbreak of Ebola virus disease in West Africa. data


ebolaModel(
  country = c("GIN", "LBR", "SLE"),
  data = NULL,
  timestep = 1/8,
  nstageE = 3L,
  R0 = 1.4,
  rho = 0.2,
  cfr = 0.7,
  k = 0,
  index_case = 10,
  incubation_period = 11.4,
  infectious_period = 7
)

Arguments

country: ISO symbol for the country (GIN=Guinea, LBR=Liberia, SLE=Sierra Leone).
data: if NULL, the situation report data (WHO Ebola Response Team 2014) for the appropriate country or region will be used. Providing a dataset here will override this behavior.
timestep: duration (in days) of Euler timestep for the simulations.
nstageE: integer; number of incubation stages.
R0: basic reproduction ratio
rho: case reporting efficiency
cfr: case fatality rate
k: dispersion parameter (negative binomial size parameter)
index_case: number of cases on day 0 (2014-04-01)
incubation_period, infectious_period: mean duration (in days) of the incubation and infectious periods.

Details

The data include monthly case counts and death reports derived from WHO situation reports, as reported by the U.S. CDC. The models are described in King et al. (2015).

The data-cleaning script is included in the R source code file ebola.R .

Model structure

The default incubation period is supposed to be Gamma distributed with shape parameter nstageE and mean 11.4 days and the case-fatality ratio (cfr) is taken to be 0.7 (cf. WHO Ebola Response Team 2014). The discrete-time formula is used to calculate the corresponding alpha (cf. He et al. 2010).

The observation model is a hierarchical model for cases and deaths:

p(R_t, D_t| C_t) = p(R_t | C_t) p(D_t | C_t, R_t).

Here, $p(R_t | C_t)$ is negative binomial with mean $\rho C_t$ and dispersion parameter $1/k$ ; $p(D_t | C_t, R_t)$ is binomial with size $R_t$ and probability equal to the case fatality rate cfr.

Examples


# takes too long for R CMD check
  if (require(ggplot2) && require(tidyr)) {
    
    ebolaWA2014 |>
      pivot_longer(c(cases,deaths)) |>
      ggplot(aes(x=date,y=value,group=name,color=name))+
      geom_line()+
      facet_grid(country~.,scales="free_y")+
      theme_bw()+
      theme(axis.text=element_text(angle=-90))
    
  }
  
  plot(ebolaModel(country="SLE"))
  plot(ebolaModel(country="GIN"))
  plot(ebolaModel(country="LBR"))

References

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. tools:::Rd_expr_doi("10.1098/rspb.2015.0347") .

WHO Ebola Response Team. Ebola virus disease in West Africa---the first 9 months of the epidemic and forward projections. New England Journal of Medicine 371 , 1481--1495, 2014. tools:::Rd_expr_doi("10.1056/NEJMoa1411100") .

D. He, E.L. Ionides, and A.A. King. Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. Journal of the Royal Society Interface 7 , 271--283, 2010. tools:::Rd_expr_doi("10.1098/rsif.2009.0151") .

ebola function