Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches

Documentation for package ‘linelistBayes’ version 1.0

backnow_cm	Get Bayesian Back-calculation Estimates and Model Diagnostics
convert_to_linelist	Convert Case Counts to a Line List
create_caseCounts	Create a Case Counts Data Frame
create_linelist	Create a Line List from Report and Onset Dates
dnb	Calculate Log-Probability Density for Negative Binomial Distribution
dummy	Generate Dummy Variables Matrix for Weeks and Weekends
findmiss	Locate Missing Values in a Numeric Vector
getr	Calculate Time-Varying Reproduction Number R(t)
get_mu_vec	Calculate Exponential of Linear Combinations
lambda	Calculate Lambda Values for Poisson Distribution Mean
logLikNB	Compute Log-Likelihood for a Right-Truncated Negative Binomial Model
out_list_demo	Sample datasets
plot.backnow	Plot Estimates or Reproduction Numbers
plot.caseCounts	Plot Case Counts Over Time
pnb	Compute Cumulative Distribution Function for Negative Binomial Distribution
prop	Calculate Proportions of Event Counts Within a Specified Time Range
rnb	Generate Random Samples from a Negative Binomial Distribution
run_backnow	Run Back Calculation and Estimate Reproduction Numbers
sample_cases	Sample datasets
sample_dates	Sample datasets
sample_location	Sample datasets
sample_onset_dates	Sample datasets
sample_report_dates	Sample datasets
si	Calculate Serial Interval Distribution for COVID-19