touchstone/script.R

In mrc-ide/malariasimulation: An individual based model for malaria

library(magrittr)

touchstone::branch_install()

touchstone::benchmark_run(
  small_population = {
    set.seed(123)
    params <- malariasimulation::get_parameters(
      overrides = list(human_population=1e4))
    malariasimulation::run_simulation(10000, params)
  },
  n = 10
)

touchstone::benchmark_run(
  large_population = {
    set.seed(123)
    params <- malariasimulation::get_parameters(
      overrides = list(human_population=1e6))
    malariasimulation::run_simulation(1000, params)
  },
  n = 4
)

touchstone::benchmark_analyze()

# Overwrite the plots generated by touchstone with something more sensible.
touchstone::benchmark_ls() %>%
  dplyr::reframe(touchstone::benchmark_read(name, branch)) %>%
  dplyr::mutate(branch=as.factor(branch), name=as.factor(name)) %>%
  dplyr::group_by(name) %>%
  dplyr::group_walk(function(data, key) {
    ggplot2::ggplot(data, ggplot2::aes(y = branch, x = elapsed, color = branch)) +
      ggplot2::geom_boxplot() +
      ggplot2::geom_jitter(height = 0.2) +
      ggplot2::guides(color="none") +
      ggplot2::labs(x="Elapsed time", y="Branch") +
      bench::scale_x_bench_time(base = NULL) +
      ggplot2::ggtitle(key$name)

    fs::path(touchstone::dir_touchstone(), "plots", key$name) %>%
      fs::path_ext_set("png") %>%
      ggplot2::ggsave(height=3)
  })