In pahanc/malariasimulation_Ace_params: An individual based model for malaria

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

suppressPackageStartupMessages(library(ggplot2))
library(malariasimulation)
library(malariaEquilibrium)

Set up some baseline parameters:

year <- 365
sim_length <- 2 * year
human_population <- 1000

simparams <- get_parameters(list(human_population = human_population))
simparams <- set_drugs(simparams, list(AL_params, DHA_PQP_params))

Run the model for some starting EIRs and fts:

outputs <- list()
starting_EIR <- 10
fts <- c(0, .25, .5, .75, 1.)

for (ft in fts) {
  simparams <- set_clinical_treatment(simparams, 1, 1, ft / 2)
  simparams <- set_clinical_treatment(simparams, 2, 1, ft / 2)
  simparams <- set_equilibrium(simparams, starting_EIR)
  output <- run_simulation(sim_length, simparams)
  # cut out the warmup
  output <- output[output$timestep > year,]
  outputs[[length(outputs) + 1]] <- output
}

Let's plot the effect of ft on PfPR2-10:

df <- do.call('rbind', lapply(seq_along(outputs), function(i) {
  df <- outputs[[i]][c('timestep', 'n_detect_730_3650', 'n_730_3650')]
  df$ft <- fts[[i]]
  df
}))

ggplot(df) + geom_line(
  aes(x = timestep, y = (n_detect_730_3650/n_730_3650), colour = ft)) + 
  labs(x = "timestep", y = "PfPR2-10")