WhiteLabRt - Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting
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>.
Last updated 3 months ago
5.30 score 5 stars 4 scripts 147 downloadslinelistBayes - Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches
Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.
Last updated 7 months ago
5.08 score 4 stars 2 scripts 443 downloads