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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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.