inst/onerun.R

In noamross/spore: Equation-free modeling of spore-driven disease dynamics

#devtools::load_all(".")
library(spore)
library(dplyr)
library(tidyr)
library(magrittr)
library(ggplot2)
library(noamtools)
library(nloptr)
library(polynom)
library(parallel)
library(rlist)

closeAllConnections()
parms = list(
  max_i = 100,
  is = 0:100,
  lambda = 0.001,
  lambda_ex = 0.2,
  alpha = 0.1,
  alpha_power = 1,
  mu = 0.01,
  r = 0.5,
  d = 0.01,
  K = 100,
  init_pop = 100,
  time_max = 40,
  prevent_inf = 0,
  prevent_ex = 0,
  macro_timestep = 0.1,
  micro_timestep = 1,
  micro_relax_steps = 0,
  project = FALSE,
  n_sims = 25000,
  control_min = 0,
  control_max = 1000,
  v = 50,
  c = 200,
  progress = TRUE,
  micro_record = 0
  #micro_record = file("micro.txt", open="w+")
  #  macro_record = file("macro.txt", open="w")
)


micro_state = c(100, 0, rep(0, parms$max_i - 1))
macro_state = restrict.micro_state(micro_state)
shadow_state = c(97.57118, -174.8631)
time = 0
#parms$control_max = 0
#determine_control(macro_state = macro_state, parms = parms, shadow_state = shadow_state, time = time, control_guess = 3, verbose = TRUE)
#Rprof("opt.prof")
#b = macro_state_c_runopt(macro_state_init = macro_state, parms=parms, shadow_state_init=shadow_state, time=0, control_guess_init=3)
#Rprof(NULL)
#saveRDS(b, "onerun.rds", compress = FALSE)