In dd-harp/MicroMoB: Discrete Time Systems for Robust Analytics for Malaria Policy (RAMP), and Transmission Dynamics and Control of Mosquito-Borne Pathogens Transmission

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

library(ramp.dts)
#devtools::load_all()

rm1 <- dts_setup()
rm1$Lpar[[1]]$scale = 200

dts_solve(rm1, Tmax=730) -> rm1

dts_steady(rm1) -> rm1

with(rm1$outputs$orbits$MYZ[[1]], {
  plot(time, M, type = "l") 
  lines(time, U, col = "darkblue") 
  lines(time, Y, col = "purple") 
  lines(time, Z, col = "darkred") 
})

with(rm1$outputs$orbits$XH[[1]], {
  plot(time, I, type = "l", ylim = c(0, 1000)) 
  lines(time, S, col = "darkblue") 
})

#devtools::load_all()
rm10 <- dts_setup(nPatches = 10, membership = 1:10, HPop = rep(100, 10), residence = c(1:10), MYZopts = list(sigma = 0.01))
rm10$Lpar[[1]]$scale = 1.5^c(-1:8) 
dts_solve(rm10, Tmax=730) -> rm10

with(rm10$outputs$orbits$XH[[1]], {
  plot(time, I[,10], type = "l", ylim = c(0, 100), col = "darkred") 
  lines(time, S[,10], col = "darkblue") 
  for(i in 2:10){
    lines(time, I[,i], col = "darkred") 
    lines(time, S[,i], col = "darkblue") 
  }
})

dd-harp/MicroMoB documentation built on June 6, 2024, 4:43 p.m.