analysis/01_epidemic_tracectories_and_counterfactuals/4_Figure_1_Meff_Meff_pl_Illustrative_Relationship.R

In mrc-ide/global-lmic-meffs: Analysis of LMIC COVID-19 Meffs

# Loading Required Librairs 
library(patchwork)

# Examining Impact of Meff on Relationship Between Mobility and Transmission 
mobility <- seq(1, -1, -0.1)
meff_values <- c(-10, -8, -6, -5, -4, -3, -2, -1, 0)
for (i in 1:9) {
  if (i == 1) {
    x <- R0 * 2 * plogis(-mobility * meff_values[i])
    df <- data.frame(Meff = rep(meff_values[i], length(x)),
                     Rt = x, 
                     mobility = mobility)
  } else {
    x <- R0 * 2 * plogis(-mobility * meff_values[i])
    df <- rbind(df, 
                data.frame(Meff = rep(meff_values[i], length(x)),
                           Rt = x, 
                           mobility = mobility))
  }
}

df_2 <- df %>%
  mutate(Meff = factor(Meff))
a <- ggplot(df_2, aes(x = mobility, y = Rt, col = Meff)) +
  geom_path() +
  lims(y = c(0, 6), x = c(1, -1)) +
  scale_colour_manual(values = rev(blues9)) +
  theme(legend.position = "none")
  
# Examining the Impact of Meff_pl Given a Particule Value of Meff
down_indices <- 1:11
up_indices <- 12:22
overall_mobility <- c(seq(1, 0, -0.1), rev(seq(1, 0, -0.1)))
upwards_mobility <- c(rep(0, length(down_indices)), rev(seq(1, 0, -0.1)))

one_Meff <- 3
one_Meff_pl <- 0
one_Rt <- R0 * 2 * plogis((-one_Meff * (1 - overall_mobility))  -  (one_Meff_pl * (upwards_mobility)))

two_Meff <- 3
two_Meff_pl <- 1
two_Rt <- R0 * 2 * plogis((-two_Meff * (1 - overall_mobility))  -  (two_Meff_pl * (upwards_mobility)))

three_Meff <- 3
three_Meff_pl <- 3
three_Rt <- R0 * 2 * plogis((-three_Meff * (1 - overall_mobility))  -  (three_Meff_pl * (upwards_mobility)))

df <- data.frame(Rt = c(one_Rt, two_Rt, three_Rt),
                 time = rep(1:22, 3),
                 Meff = c(rep(one_Meff, length(one_Rt)), rep(two_Meff, length(two_Rt)), rep(three_Meff, length(three_Rt))),
                 Meff_pl = c(rep(one_Meff_pl, length(one_Rt)), rep(two_Meff_pl, length(two_Rt)), rep(three_Meff_pl, length(three_Rt))))
df <- df %>%
  mutate(Meff_pl = factor(Meff_pl))

b <- ggplot(df, aes(x = time, y = Rt)) +
  geom_path() +
  facet_grid(Meff_pl~.) +
  theme(strip.background = element_blank(),
        strip.text = element_blank())

a + b