Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting
Convert Case Counts to a Line List
Create a Case Counts Data Frame
Create a Line List from Report and Onset Dates
Plot Estimates or Reproduction Numbers
Plot Case Counts Over Time
Run Back Calculation and Estimate Reproduction Numbers
Calculate a Serial Interval Distribution
Run Spatial R(t) estimation and Estimate Reproduction Numbers
The 'WhiteLabRt' package.
A collection of functions related to novel methods for estimating R(t), created by the lab of Professor Laura White. Currently implemented methods include two-step Bayesian back-calculation and now-casting for line-list data with missing reporting delays, adapted in 'STAN' from Li (2021) <doi:10.1371/journal.pcbi.1009210>, and calculation of time-varying reproduction number assuming a flux between various adjacent states, adapted into 'STAN' from Zhou (2021) <doi:10.1371/journal.pcbi.1010434>.