data-raw/agents_sims.R

In skgallagher/timeternR: A Pipeline to Analyze and Compare Infectious Disease Epidemics

library(dplyr)
library(tidyr)
library(ggtern)
devtools::load_all()


set.seed(2019)
n_sims <- 50
n_time_steps <- 50
#beta <- .4
#gamma <- .12
beta <- .2
gamma <- .06
init_SIR <- c(187, 1, 0)
output_format <- "array"

agents_sims <- simulate_SIR_agents(n_sims = n_sims,
                           n_time_steps = n_time_steps,
                           beta = beta, gamma = gamma,
                           init_SIR = init_SIR)

all_sims_agg <- agents_sims %>%
 group_by(sim) %>%
    EpiCompare::agents_to_aggregate_SIR(ind = 1:3)

library(ggplot2)
ggplot(data = all_sims_agg, aes(x = t, y = S, col = as.numeric(sim),
                                group = sim)) +
                            geom_line()



usethis::use_data(agents_sims, overwrite = TRUE)