Specifying multi-stage interventions
EPICYST can incorporate complex interventions, whereby different interventions and/or characteristics of interventions can be modified in a second stage. An example of a multi-stage intervention could be focussed on treating/vaccinating all pigs with a first intervention round, followed by treatment/vaccination in only young, susceptible pigs that enter the system in subsequent rounds (as proposed in CYSTINET-AFRICA, 2019) - Figure 1 below outlines such an intervention and how this works in EPICYST.
A multi-stage intervention can be specified as follows:
intervention_frequency_stage1 and
intervention_frequency_stage2;
intervention_time_stage1 and
intervention_time_stage2; specifying the
num_intervention_rounds_stage1 and
num_intervention_rounds_stage1, and specifying coverage and
age-group targets for pig interventions (as outlined in Figure 1):
# Run pig MDA
ci1 <- run_model(time = 11, burn_in = 100, intervention_stage1 = c('Pig_MDA','Pig_vaccine'),
intervention_stage2 = c('Pig_MDA','Pig_vaccine'),
intervention_time_stage1 =1, intervention_frequency_stage1 = 3,
num_intervention_rounds_stage1 = 1, num_intervention_rounds_stage2 = 6,
intervention_time_stage2 =1.25, intervention_frequency_stage2 = 6,
pig_MDA_cov_stage1 = 0.9, pig_MDA_cov_stage2 = 0.75,
pig_vaccine_ds1_cov_stage2 = 0.75, pig_vaccine_ds2_cov_stage2 = 0.75,
pig_vaccine_ds1_cov_stage1 = 0.9, pig_vaccine_ds2_cov_stage1 = 0.9,
age_target_pig_MDA_stage1 = c(4:150), age_target_pig_MDA_stage2 = c(4:7),
age_target_pig_vaccine_stage1 = c(4:150), age_target_pig_vaccine_stage2 = c(4:7))# Plot the output in base R; pig MDA
plot(ci1$Pig_Cysticercosis_prev*100 ~ ci1$t, type = "l", col = "blue", ylim = c(0,15),
ylab = 'prevalence (%)', xlab = 'time (months)')
lines(ci1$Human_Cysticercosis_prev*100 ~ ci1$t, type = "l", col = "red")
lines(ci1$Human_Taeniasis_prev*100 ~ ci1$t, type = "l", col = "green")
legend('topright', c('Porcine cysticercosis','Human cysticercosis', 'Human taeniasis'), lty = c(1,1,1),
col=c('blue','red','green'))