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

## Documentation for package ‘EpiNow2’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M O P R S T U misc

## -- A --

add_day_of_week | Adds a day of the week vector
adjust_infection_to_report | Adjust from Case Counts by Infection Date to Date of Report
allocate_delays | Allocate Delays into Required Stan Format
allocate_empty | Allocate Empty Parameters to a List

## -- B --

backcalc_opts | Back Calculation Options
bootstrapped_dist_fit | Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters

## -- C --

c.dist_spec | Combines multiple delay distributions for further processing
calc_CrI | Calculate Credible Interval
calc_CrIs | Calculate Credible Intervals
calc_summary_measures | Calculate All Summary Measures
calc_summary_stats | Calculate Summary Statistics
clean_nowcasts | Clean Nowcasts for a Supplied Date
clean_regions | Clean Regions
construct_output | Construct Output
convert_to_logmean | Convert mean and sd to log mean for a log normal distribution
convert_to_logsd | Convert mean and sd to log standard deviation for a log normal distribution
copy_results_to_latest | Copy Results From Dated Folder to Latest
create_backcalc_data | Create Back Calculation Data
create_clean_reported_cases | Create Clean Reported Cases
create_future_rt | Construct the Required Future Rt assumption
create_gp_data | Create Gaussian Process Data
create_initial_conditions | Create Initial Conditions Generating Function
create_obs_model | Create Observation Model Settings
create_rt_data | Create Time-varying Reproduction Number Data
create_shifted_cases | Create Delay Shifted Cases
create_stan_args | Create a List of Stan Arguments
create_stan_data | Create Stan Data Required for estimate_infections
create_stan_delays | Create delay variables for stan

## -- D --

delay_opts | Delay Distribution Options
dist_fit | Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions
dist_skel | Distribution Skeleton
dist_spec | Specify a distribution.
dist_spec_plus | Creates a delay distribution as the sum of two other delay distributions

## -- E --

epinow | Real-time Rt Estimation, Forecasting and Reporting
estimates_by_report_date | Estimate Cases by Report Date
estimate_delay | Estimate a Delay Distribution
estimate_infections | Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
estimate_secondary | Estimate a Secondary Observation from a Primary Observation
estimate_truncation | Estimate Truncation of Observed Data
example_confirmed | Example Confirmed Case Data Set
expose_stan_fns | Expose internal package stan functions in R
extract_CrIs | Extract Credible Intervals Present
extract_inits | Generate initial conditions from a Stan fit
extract_parameter | Extract Samples for a Parameter from a Stan model
extract_parameter_samples | Extract Parameter Samples from a Stan Model
extract_stan_param | Extract a Parameter Summary from a Stan Object
extract_static_parameter | Extract Samples from a Parameter with a Single Dimension

## -- F --

filter_opts | Filter Options for a Target Region
fit_model_with_nuts | Fit a Stan Model using the NUTs sampler
fit_model_with_vb | Fit a Stan Model using Variational Inference
forecast_secondary | Forecast Secondary Observations Given a Fit from estimate_secondary
format_fit | Format Posterior Samples

## -- G --

gamma_dist_def | Generate a Gamma Distribution Definition Based on Parameter Estimates
generation_times | Literature Estimates of Generation Times
generation_time_opts | Generation Time Distribution Options
get_dist | Get a Literature Distribution
get_generation_time | Get a Literature Distribution for the Generation Time
get_incubation_period | Get a Literature Distribution for the Incubation Period
get_raw_result | Get a Single Raw Result
get_regional_results | Get Combined Regional Results
get_regions | Get Folders with Results
get_regions_with_most_reports | Get Regions with Most Reported Cases
get_seeding_time | Estimate seeding time from delays and generation time
gp_opts | Approximate Gaussian Process Settings
growth_to_R | Convert Growth Rates to Reproduction numbers.

## -- I --

incubation_periods | Literature Estimates of Incubation Periods
init_cumulative_fit | Generate initial conditions by fitting to cumulative cases

## -- L --

lognorm_dist_def | Generate a Log Normal Distribution Definition Based on Parameter Estimates

## -- M --

make_conf | Format Credible Intervals
map_prob_change | Categorise the Probability of Change for Rt
match_output_arguments | Match User Supplied Arguments with Supported Options
mean.dist_spec | Returns the mean of one or more delay distribution

## -- O --

obs_opts | Observation Model Options
opts_list | Return an _opts List per Region

## -- P --

plot | Plot method for estimate_infections
plot.dist_spec | Plot PMF and CDF for a dist_spec object
plot.epinow | Plot method for epinow
plot.estimate_infections | Plot method for estimate_infections
plot.estimate_secondary | Plot method for estimate_secondary
plot.estimate_truncation | Plot method for estimate_truncation
plot_CrIs | Plot EpiNow2 Credible Intervals
plot_estimates | Plot Estimates
plot_summary | Plot a Summary of the Latest Results
print.dist_spec | Prints the parameters of one or more delay distributions
process_region | Process regional estimate
process_regions | Process all Region Estimates

## -- R --

regional_epinow | Real-time Rt Estimation, Forecasting and Reporting by Region
regional_runtimes | Summarise Regional Runtimes
regional_summary | 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
rstan_opts | Rstan Options
rstan_sampling_opts | Rstan Sampling Options
rstan_vb_opts | Rstan Variational Bayes Options
rt_opts | Time-Varying Reproduction Number Options
run_region | Run epinow with Regional Processing Code
R_to_growth | Convert Reproduction Numbers to Growth Rates

## -- S --

sample_approx_dist | Approximate Sampling a Distribution using Counts
save_estimate_infections | Save Estimated Infections
save_input | Save Observed Data
secondary_opts | Secondary Reports Options
setup_default_logging | Setup Default Logging
setup_dt | Convert to Data Table
setup_future | Set up Future Backend
setup_logging | Setup Logging
setup_target_folder | Setup Target Folder for Saving
simulate_infections | Simulate infections using a given trajectory of the time-varying reproduction number
simulate_secondary | Simulate a secondary observation
stan_opts | Stan Options
summarise_key_measures | Summarise rt and cases
summarise_results | Summarise Real-time Results
summary | Summary output from epinow
summary.epinow | Summary output from epinow
summary.estimate_infections | Summary output from estimate_infections

## -- T --

trunc_opts | Truncation Distribution Options

## -- U --

update_horizon | Updates Forecast Horizon Based on Input Data and Target
update_list | Update a List
update_secondary_args | Update estimate_secondary default priors

## -- misc --

+.dist_spec | Creates a delay distribution as the sum of two other delay distributions