In jrcpulliam/LLsim: Line List Simulator

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This vignette shows how to generate simulated line lists using the LLsim package, and how to visulize the output using the incidence and epicontacts packages from the R Epidemics Consortium (RECON). We start by loading the LLsim library:

library(LLsim)

if (!requireNamespace("incidence", quietly = TRUE)){
  stop("Package \"incidence\" needed for this vignette to work. Please install it.",
       call. = FALSE)
  }
if (!requireNamespace("epicontacts", quietly = TRUE)){
  stop("Package \"epicontacts\" needed for this vignette to work. Please install it.",
       call. = FALSE)
  }

The epidemic simulation is done using the simpleSim() function, as follows:

out <- simpleSim(inc_mean_param = 4.5,
                 inf_mean_param = 5,
                 R_0 = 1.3,
                 case_fatality = .17,
                 pop_size = 100,
                 inc_shape_param = 2.3,
                 inf_shape_param = 2.3,
                 seed = 53274828)

The parameters of the incubation and infectious period distributions used for this simulation represent estimates for pnuemonic plague in India, as described in Joshi et al. (2009) Trans Roy Soc Trop Med Hyg 103: 455-460 (link). The $R_0$ value is set based on the estimate of Gani and Leach (2004) Emerg Infect Dis 10(4): 608-614 (link).

The function returns two objects: pop, which has r nrow(out$pop) rows, each representing an individual in the population, and cases, which has r nrow(out$cases) rows, each representing an individual infected during the course of the simulated epidemic.

Next, we use the function createLineList() to create a line list of observed cases from the set of all cases, as follows:

ll <- createLineList(out$cases,
                     obs_prob = 0.8,
                     mean_report_delay = 2,
                     mean_confirm_delay = 4,
                     zero_date = '2019-01-02',
                     obs_date = '2020-01-30')

Because the individual observation probability was set to 0.8, not all cases that occurred appear in the line list, which only has r nrow(ll) rows. The line list generated has the following structure:

knitr::kable(head(ll, 10), row.names = FALSE)

Now that we have a simulated line list, we can use it to generate visualizations via the incidence and epicontacts packages, as follows:

inc <- incidence::incidence(dates = ll$onsetDate, interval = 'week')
plot(inc)

ec <- epicontacts::make_epicontacts(ll, subset(ll, select = c('caseID','source')), id = 1L, from = 2L, to = 1L, directed = TRUE)
plot(ec)

jrcpulliam/LLsim documentation built on Feb. 5, 2020, 8:49 p.m.