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fig_age_dist.R
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fig_age_dist.R
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# Requires testC and testU from fig_hypotheses.R
age_distC = dcast(testC$dynamics[population %in% c("East of England", "South East", "London") & t %between% c(335, 366),
.(s1 = sum(Ip + Is + Ia), s2 = sum(Ip2 + Is2 + Ia2)), by = .(population, group, run)][,
.(age = group * 5 - 2.5, s1 = s1 / sum(s1), s2 = s2 / sum(s2)), by = .(population, run)][,
.(variant = rep(c("Preexisting", "VOC 202012/01"), each = 3),
value = c(quantile(s1, c(0.025, 0.5, 0.975)), quantile(s2, c(0.025, 0.5, 0.975))),
q = rep(c("lo", "mid", "hi"), 2)), by = .(age)], age + variant ~ q)
age_distU = dcast(testU$dynamics[population %in% c("East of England", "South East", "London") & t %between% c(335, 366),
.(s1 = sum(Ip + Is + Ia), s2 = sum(Ip2 + Is2 + Ia2)), by = .(population, group, run)][,
.(age = group * 5 - 2.5, s1 = s1 / sum(s1), s2 = s2 / sum(s2)), by = .(population, run)][,
.(variant = rep(c("Preexisting", "VOC 202012/01"), each = 3),
value = c(quantile(s1, c(0.025, 0.5, 0.975)), quantile(s2, c(0.025, 0.5, 0.975))),
q = rep(c("lo", "mid", "hi"), 2)), by = .(age)], age + variant ~ q)
age_distC[, age := (age %/% 10) * 10 + 5]
age_distC = age_distC[, lapply(.SD, sum), by = .(age, variant)]
age_distU[, age := (age %/% 10) * 10 + 5]
age_distU = age_distU[, lapply(.SD, sum), by = .(age, variant)]
plot_ageC = ggplot(age_distC) +
geom_col(aes(age, mid, fill = variant, group = variant), position = "dodge") +
geom_linerange(aes(age, ymin = lo, ymax = hi, group = variant), position = position_dodge(width = 10)) +
labs(x = "Age", y = "Proportion of infections", fill = "Variant") +
theme_cowplot() + theme(legend.position = c(0.05, 0.9)) + ylim(0, 0.35)
plot_ageU = ggplot(age_distU) +
geom_col(aes(age, mid, fill = variant, group = variant), position = "dodge") +
geom_linerange(aes(age, ymin = lo, ymax = hi, group = variant), position = position_dodge(width = 10)) +
labs(x = "Age", y = "Proportion of infections", fill = "Variant") +
theme_cowplot() + theme(legend.position = c(0.05, 0.9)) + ylim(0, 0.35)
dS = fread("~/Documents/newcovid/data/sgtf_agedist.csv") # from PHE Pillar 2 testing data
dS[, variant := c("S gene present", "S gene target failure")[sgtf + 1]]
plot_ageE = ggplot(dS) +
geom_col(aes(ag0, mean, fill = variant, group = variant), position = "dodge") +
geom_linerange(aes(ag0, ymin = lo, ymax = hi, group = variant), position = position_dodge(width = 10)) +
labs(x = "Age", y = "Proportion of cases", fill = "Variant") +
theme_cowplot() + theme(legend.position = c(0.05, 0.9)) + ylim(0, 0.35)
p1 = plot_ageU + labs(title = "Longer infectious period")
p2 = plot_ageC + labs(title = "Increased susceptibility among children")
p3 = plot_ageE + labs(title = "Pillar 2 testing data")
cowplot::plot_grid(p1, p2, p3, nrow = 2, labels = LETTERS, label_size = 14)
ggsave("./output/age_dist_model.pdf", width = 35, height = 28, units = "cm", useDingbats = FALSE)
ggsave("./output/age_dist_model.png", width = 35, height = 28, units = "cm")