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library(malariasimulation)
library(magenta)
library(tictoc)

EIR <- 50 
ft <- 0.5 
N <- 500000
timesteps = 30

# malariasimulation should have individual mosquiotes on for fair comparison
params <- malariasimulation::get_parameters(overrides = list("human_population" = N, "individual_mosquitoes" = TRUE)) |> 
  malariasimulation::set_equilibrium(init_EIR = EIR)

# set the mosquito limit the same so not populating unnecessary of mosquitoes
params$mosquito_limit <- params$total_M

#Update parameter set with chosen drug-specific parameters (AL)
drug_params <- malariasimulation::set_drugs(params, list(AL_params))

# Set treatment program for AL (drug index = 1)
treatment_params <- malariasimulation::set_clinical_treatment(
  parameters = drug_params,
  drug = 1,
  timesteps =  c(0), # Treatment coverage at day 0 = ft
  coverages =  c(ft))

# Use set_equilibrium to update the parameter set for a given initial EIR
treatment_params <- malariasimulation::set_equilibrium(treatment_params, EIR)

tictoc::tic()
test_sim_eq <- malariasimulation::run_simulation(timesteps = timesteps, parameters = treatment_params)
tictoc::toc()
#> 80.06 sec elapsed

# here we compare against magenta, with update_save on (rendering) and update_length set to 1 (to render every day)
tictoc::tic()
test_simmag <- magenta::pipeline(EIR = EIR, ft = ft, N = N, update_save = TRUE, update_length = 1, years = timesteps/365)
#> Seed set to 222651067
#> magenta v1.3.5
#> Starting Stochastic Simulation for 0.0821917808219178 years
tictoc::toc()
#> 45.777 sec elapsed