Add seasonal/perennial vector mix example to set_carrying_capacity vignette

[pwinskill]

The set carrying capacity help should inform the user

1. How to recreate the internal seasonality dynamics with set_carrying_capacity()
2. How to model a mix of seaonal and perennial vectors.

Sandbox example:

library(malariasimulation)

# Some seasonal pars
g0 <- 0.284596
g <- c(-0.317878, -0.0017527, 0.116455)
h <- c(-0.331361, 0.293128, -0.0617547)

# Setting seasonality the standard way
p_seasonal <- get_parameters(
  list(
    human_population = 10000,
    model_seasonality = TRUE,
    g0 = g0,
    g = g,
    h = h
  )
) |>
  set_equilibrium(init_EIR = 20)
p_seasonal$clinical_incidence_rendering_min_ages = 0
p_seasonal$clinical_incidence_rendering_max_ages = 100 * 365

s_seasonal <- run_simulation(365 * 5, p_seasonal)

# Setting seasonality via carrying capacity (dev branch version)
r <- rep(NA, 365 * 5)
for(t in 1:(365 * 5)){
  r[t] <- malariasimulation:::rainfall(
    t,
    g0,
    g,
    h,
    0.001
  )
}
r_bar <- mean(r)

p_cc <- get_parameters(
  list(
    human_population = 10000
  )
) |>
  set_carrying_capacity(
    timesteps = 1:(365 * 5),
    carrying_capacity_scalers <- 
      matrix(r / r_bar, ncol = 1)
  )  |>
  set_equilibrium(init_EIR = 20)
p_cc$clinical_incidence_rendering_min_ages = 0
p_cc$clinical_incidence_rendering_max_ages = 100 * 365

s_cc <- run_simulation(365 * 5, p_cc)

# With perennial sp alongside seasonal

sea <- malariasimulation::gamb_params
sea$species <- "seasonal"

per <- malariasimulation::gamb_params
per$species <- "perennial"

p_cc2 <- get_parameters(
  list(
    human_population = 10000
  )
) |>
  set_species(list(
    sea = sea,
    per = per
  ),
  proportions = c(0.5, 0.5)
  ) |>
  set_carrying_capacity(
    timesteps = 1:(365 * 5),
    carrying_capacity_scalers <- 
      matrix(c(r / r_bar, rep(1, length(r))), ncol = 2)
  )  |>
  set_equilibrium(init_EIR = 20)
p_cc2$clinical_incidence_rendering_min_ages = 0
p_cc2$clinical_incidence_rendering_max_ages = 100 * 365

s_cc2 <- run_simulation(365 * 5, p_cc2)


# Compare incidence
par(mfrow = c(1, 2))
# Standard seasonal
plot(s_seasonal$n_inc_clinical_0_36500, t = "l", ylab = "inc")
# Recreating seasonal with carrying capacity changes
lines(s_cc$n_inc_clinical_0_36500, col = "red")
# One seasonal and one perennial vector
lines(s_cc2$n_inc_clinical_0_36500, col = "green")

# Compare EIR
plot(s_cc2$EIR_seasonal, t = "l", ylab = "EIR")
lines(s_cc2$EIR_perennial, col = "green")