Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters


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Documentation for package ‘EpiNow2’ version 1.1.0

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adjust_infection_to_report Adjust from Case Counts by Infection Date to Date of Report
bootstrapped_dist_fit Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters
clean_nowcasts Clean Nowcasts for a Supplied Date
country_map Generate a country map for a single variable.
covid_generation_times Covid Generation Time Estimates
covid_incubation_period Covid Incubation Period
covid_serial_intervals Covid Generation Serial Intervals
dist_fit Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions
dist_skel Distribution Skeleton
epinow Real-time Rt Estimation, Forecasting and Reporting
estimate_infections Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
example_confirmed Example Confirmed Case Data Set
forecast_infections Forecast Infections and the Time-Varying Reproduction Number
gamma_dist_def Generate a Gamma Distribution Definition Based on Parameter Estimates
get_raw_result Get a Single Raw Result
get_regional_results Get Combined Regional Results
get_regions Get Folders with Nowcast Results
global_map Generate a global map for a single variable.
growth_to_R Convert Growth Rates to Reproduction numbers.
lognorm_dist_def Generate a Log Normal Distribution Definition Based on Parameter Estimates
make_conf Format Credible Intervals
map_prob_change Categorise the Probability of Change for Rt
plot_estimates Plot Estimates
plot_summary Plot a Summary of the Latest Results
regional_epinow Real-time Rt Estimation, Forecasting and Reporting by Region
regional_summary Generate Regional Summary Output
report_cases Report case counts by date of report
report_plots Report plots
report_summary Provide Summary Statistics for Estimated Infections and Rt
R_to_growth Convert Reproduction Numbers to Growth Rates
sample_approx_dist Approximate Sampling a Distribution using Counts
simulate_cases Simulate Cases by Date of Infection, Onset and Report
summarise_key_measures Summarise rt and cases
summarise_results Summarise Real-time Results
theme_map Custom Map Theme