sim.epidemic: Simulation of an epidemic in space and time In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Description

A function which simulates the spatial spread of infections through time given the reproductive number (`R`), a function describing the spatial transmission kernel (`trans.kern.func`), and the mean and standard deviation of the generation time distribution (`gen.t.mean` and `gen.t.sd`) for the infecting pathogen. The function returns the location (`x`, `y`) and time (`t`) for each case of infection in the simulation.

Usage

 ```1 2``` ```sim.epidemic(R, gen.t.mean, gen.t.sd, trans.kern.func, tot.generations = 10, min.cases = 0, max.try = 1000) ```

Arguments

 `R` a scalar or a vector of length `tot.generations` providing the reproductive number for the epidemic. If scalar, the R value is constant. If a vector, the R value varies according to each generation in the vector. `gen.t.mean` mean of generation time `gen.t.sd` standard deviation of the generation time (assumed to be normally distributed) `trans.kern.func` a function for the transmission kernel that takes `n` as an arguement. Function and associated parameters must be given in a list object. `tot.generations` the total number of generations in the epidemic, where the index case (x,y,t = [0,0,0]) is considered generation zero (default = 10) `min.cases` the minimum number of cases in the epidemic (default = 0) `max.try` maximum number of tries to acheive the minimum number of cases (default = 1000)

Value

a numerical matrix with three columns giving the coordinates `x` and `y`, and time `t` of simulated cases

Author(s)

John Giles, Justin Lessler, and Henrik Salje

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29``` ``` set.seed(1) dist.func <- alist(n=1, a=1/100, rexp(n, a)) # Exponential transmission kernel with mean = sd = 100 # Simulate epidemic with constant R value a <- sim.epidemic(R=1.5, gen.t.mean=7, gen.t.sd=2, tot.generations=15, min.cases=100, trans.kern.func=dist.func) sim.plot(a) # Simulate an epidemic with variable R value r1 <- 2 r2 <- 0.25 tg <- 25 R <- seq(r1, r2, (r2 -r1)/(tg - 1)) b <- sim.epidemic(R=R, gen.t.mean=7, gen.t.sd=2, tot.generations=tg, min.cases=100, trans.kern.func=dist.func) sim.plot(b) ```

IDSpatialStats documentation built on Nov. 16, 2019, 1:08 a.m.