A collection of functions related to novel methods for estimating reproduction number, R(t), created by the lab of Professor Laura White at Boston University School of Public Health.
Temporal R(t) estimation: Two-step Bayesian back and nowcasting for linelist data with missing reporting delays, adapted in STAN from Li and White
Remaining todos:
[] Implement the right-truncated NB distribution function in the likelihood and rng forms, see here for starters
Spatial R(t) estimation: Calculating time-varying reproduction number, R(t), assuming a flux of infectors between various adjacent states. This was adapted in STAN from Zhou and White
Remaining todos:
[] Continuing working on non-centered parameterization, AR1 process, and partial pooling [] Use tidy bayes for QC