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.
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Temporal R(t) estimation: Two-step Bayesian back and nowcasting for linelist data with missing reporting delays, adapted in STAN from Li and White
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Remaining todos:
[] Implement the right-truncated NB distribution function in the likelihood and rng forms, see here for starters
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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
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Remaining todos:
[] Continuing working on non-centered parameterization, AR1 process, and partial pooling [] Use tidy bayes for QC
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- Unified spatial-temporal R(t) estimation Combining the two methods above.
- Genetic-based R(t) Using genetic data to inform R(t) calculation