Set up graph file to run simulations upon
disnet_sim_setup(g, r0 = 1.44, latent_period = 2.62, inf_period = 3.38, tau = 3, r_beta = 0.5, p_a = 1/3, seed_nd = NA, seed_no = 1, vacc = FALSE, output_dir = getOption("disnetOutputDir", NA), vacc_eff = c(80, 90), vacc_cov = c(80, 100), vacc_nd = "890", ...)
| g | The network object created after commuting rates were calculated |
|---|---|
| r0 | Reproduction number |
| latent_period | Period between infection and becoming infectious |
| inf_period | Duration of infectious period |
| tau | Return rate (from commuting) |
| r_beta | Reduction in infectiousness due to being aymptomatic inf |
| p_a | Probability of asymptomatic infection |
| seed_nd | The node which you want to seed/initiate infection in |
| seed_no | The number of infected people you want to start inf with |
| vacc | Whether a vaccination campaign is underway or not |
| output_dir | Directory to store intermediate simulation data in. |
| vacc_eff | Vaccination efficacy |
| vacc_cov | Vaccination coverage |
| vacc_nd | Node you want to vaccinate in |
1. Reads in an `igraph` object (with commuting proportions previously calculated)
2. Calculates and attaches "Effective Population" to graph
3. Vaccinates target nodes with vaccination proportion: vaccination proportions = vaccination coverage * vaccination efficacy The proportion of a node that is vaccinated is removed from the Susceptible compartment and added to the Recovered compartment
3. Seeds a node with specified number of infectious individuals (taking them out from the Susceptibles and adding to Infectious compartment
4. Creates the FOI structure/scaffold used to quickly calculate FOI (FOI = Force of Infection, acting on an individual in a node)
f = system.file("sample_data/network", "g10.RDS", package = "SEEDNet") g = readRDS(f) g_comm = disnet_commuting(g)#> [1] "working on node: 20" #> [1] "working on node: 128" #> [1] "working on node: 358" #> [1] "working on node: 416" #> [1] "working on node: 781" #> [1] "working on node: 874" #> [1] "working on node: 890" #> [1] "working on node: 958" #> [1] "working on node: 995"nodes = igraph::vcount(g_comm) set.seed(890) seed_nd = igraph::vertex_attr(g_comm, "name", sample(1:nodes, 1)) for_sim = disnet_sim_setup(g_comm, seed_nd = seed_nd, output_dir = NA)