imuGAP: an Estimation Model for Measles Vaccination Coverage

library(imuGAP)

The name imuGAP stands for “Immunity: Geographic & Age-based Projection”, and as that name implies, the package provides a stan-based model for estimating measles vaccination coverage by location and age cohort.

The core model represents a target population as having a life-long propensity for vaccination; some proportion, $\phi$ , of that population is unlikely to vaccinate and the complementary proportion, $1 - \phi$ , is likely to vaccinate. That population then experiences a vaccination rate, $\lambda$ , over the model time eras, according to the vaccination eligibility schedule, $\nu$ . These core parameters can vary over time and location, in a user-specifiable way.

Focusing just on the core model element, imagine a particular population location $i$ and cohort $a$ (where $a$ denotes the start of the time period when that group was born). If that cohort is now age $t$ , and the vaccine schedule for the first dose is $\nu(t)$ , the expected fraction of that group to have at least one dose is then:

$P(\ge\textrm{1 dose}) = \left(1 - \phi_{i, a}\right) \left(1 - \exp\left\{-\int_a^{t} \lambda_{i, a}(s)\nu(s) d\textrm{s}\right\}\right)$

Which is to say, we are representing vaccination coverage via a survival model. Leaving aside the “unlikely” population