Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches
Get Bayesian Back-calculation Estimates and Model Diagnostics
Convert Case Counts to a Line List
Create a Case Counts Data Frame
Create a Line List from Report and Onset Dates
Calculate Log-Probability Density for Negative Binomial Distribution
Generate Dummy Variables Matrix for Weeks and Weekends
Locate Missing Values in a Numeric Vector
Calculate Exponential of Linear Combinations
Calculate Time-Varying Reproduction Number R(t)
Calculate Lambda Values for Poisson Distribution Mean
Compute Log-Likelihood for a Right-Truncated Negative Binomial Model
Plot Estimates or Reproduction Numbers
Plot Case Counts Over Time
Compute Cumulative Distribution Function for Negative Binomial Distrib...
Calculate Proportions of Event Counts Within a Specified Time Range
Generate Random Samples from a Negative Binomial Distribution
Run Back Calculation and Estimate Reproduction Numbers
Calculate Serial Interval Distribution for COVID-19
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.