In dchodge/hero-study: HERO study statistical analysis

Statistic models in paper

Model A. Seroprevalence model

Code to run the seroprevalence model.

prev <- init_model_prev("prev", "sero_pos", datafit_prev, "sero_prev")
asymp <- init_model_prev("asymp", "asymp_pos", datafit_asymp, "asymp")

fit(prev)
fit(asymp)

clean_samples(prev)
clean_samples(asymp)

plot(prev, "Seroprevalence", "Fig1") # calls clean_samples(prev)
plot(asymp, "Proportion Asymptomatic", "FigS1")  # calls clean_samples(asymp)

Model B. AB kinetics model

Code to run the antibody kinetics model.

library(posterior) 

inter_start <- c("marginal_a_i", "marginal_e_i", "marginal_g_i", "marginal_s_i")
slope_change <- c("marginal_a_s", "marginal_e_s", "marginal_g_s", "marginal_s_s")

start <- init_model_ab_kin(name = "start",
                           stan_file = "start",
                           datafit = datafit_start,
                           marginal_vars = inter_start,
                           y_axis = "log(AU) at first bleed")
change <- init_model_ab_kin(name = "change",
                            stan_file = "change",
                            datafit = datafit_change,
                            marginal_vars = slope_change,
                            y_axis = "Change in log(AU) after 28 days")

# Run the mcmc sampler on these fits
fit(start)
fit(change)

# Clean the mcmc samples
clean_samples(start)
clean_samples(change)
clean_samples_revert(start, change)

# Plot figs
plot(start)
plot(change)
plot_revert(start, change)

# Plot final figurre
plot_figure_2(start, change, 8, 8)

Model C. Hetergeneous sensitivity and specificity model

Hetergeneous sensitivity and specficity model.

sens <- test_metric("Sensitivity", 60:100, datafit_seropos, `>`)
spec <- test_metric("Specificity", 60:100, datafit_seroneg, `<`)

fit(sens)
fit(spec)

plot(sens, 10, 10, "fig3_sens")
plot(spec, 10, 10, "fig3_spec")

Plot supplementary figures

# Figure S1
plot_dates(10, 10)
# Supp to model 2
plot_correlations(10, 10)
plot_time_supp(10, 10)

# Supp to model 3
plot_od_sens_curve(10, 10)
plot_roc(10, 10)
plot_roc_age(10, 10)