# Estimate and Forecast Real-Time Infection Dynamics

## Documentation for package ‘EpiNow2’ version 1.9.0

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

## Help Pages

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

## -- A --

add_breakpoints | Add breakpoints to certain dates in a data set.
apply_zero_threshold | Convert zero case counts to 'NA' (missing) if the 7-day average is above a threshold.
as_forecast_sample | Convert EpiNow2 model output to a 'forecast_sample' object
as_forecast_sample.epinow | Convert EpiNow2 model output to a 'forecast_sample' object
as_forecast_sample.estimate_infections | Convert EpiNow2 model output to a 'forecast_sample' object
as_forecast_sample.estimate_truncation | Convert EpiNow2 model output to a 'forecast_sample' object
as_forecast_sample.forecast_secondary | Convert EpiNow2 model output to a 'forecast_sample' object

## -- B --

backcalc_opts | Back Calculation Options
bootstrapped_dist_fit | Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters
bound_dist | Define bounds of a <dist_spec>

## -- 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
collapse | Collapse nonparametric distributions in a <dist_spec>
collapse.dist_spec | Collapse nonparametric distributions in a <dist_spec>
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
convolve_and_scale | Convolve and scale a time series

## -- D --

delay_opts | Delay Distribution Options
Dirichlet | Probability distributions
discretise | Discretise a <dist_spec>
discretise.dist_spec | Discretise a <dist_spec>
discretize | Discretise a <dist_spec>
Distributions | Probability distributions
dist_fit | Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions

## -- E --

epinow | Real-time Rt Estimation, Forecasting and Reporting
epinow2_cmdstan_model | Load and compile an EpiNow2 cmdstanr model
estimate_delay | Estimate a Delay Distribution
estimate_dist | Estimate a delay distribution using primarycensored
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
example_generation_time | Example generation time
example_incubation_period | Example incubation period
example_reporting_delay | Example reporting delay
example_truncated | Example Case Data Set with Truncation
Exp | Probability distributions
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_samples | Extract all samples from a stan fit
extract_stan_param | Extract a parameter summary from a Stan object

## -- F --

fill_missing | Fill missing data in a data set to prepare it for use within the package
filter_leading_zeros | Filter leading zeros from a data set.
filter_opts | Filter Options for a Target Region
Fixed | Probability distributions
fix_parameters | Fix the parameters of a <dist_spec>
fix_parameters.dist_spec | Fix the parameters of a <dist_spec>
forecast_infections | Forecast infections from a given fit and trajectory of the time-varying reproduction number
forecast_opts | Forecast options
forecast_secondary | Forecast Secondary Observations Given a Fit from estimate_secondary

## -- G --

Gamma | Probability distributions
generation_time_opts | Generation Time Distribution Options
get_distribution | Get the distribution of a <dist_spec>
get_parameters | Get parameters from distributions or fitted models
get_parameters.dist_spec | Get parameters from distributions or fitted models
get_parameters.epinowfit | Get parameters from distributions or fitted models
get_parameters.estimate_dist | Get parameters from distributions or fitted models
get_pmf | Get the probability mass function of a nonparametric distribution
get_predictions | Get predictions from a fitted model
get_predictions.estimate_infections | Get predictions from a fitted model
get_predictions.estimate_secondary | Get predictions from a fitted model
get_predictions.estimate_truncation | Get predictions from a fitted model
get_predictions.forecast_infections | Get predictions from a fitted model
get_predictions.forecast_secondary | Get predictions from a fitted model
get_regional_results | Get Combined Regional Results
get_samples | Get posterior samples from a fitted model
get_samples.epinow | Get posterior samples from a fitted model
get_samples.estimate_infections | Get posterior samples from a fitted model
get_samples.estimate_secondary | Get posterior samples from a fitted model
get_samples.estimate_truncation | Get posterior samples from a fitted model
get_samples.forecast_infections | Get posterior samples from a fitted model
get_samples.forecast_secondary | Get posterior samples from a fitted model
gp_opts | Approximate Gaussian Process Settings
growth_to_R | Convert Growth Rates to Reproduction numbers.
gt_opts | Generation Time Distribution Options

## -- I --

is_constrained | Check if a <dist_spec> is constrained, i.e. has a finite maximum or nonzero CDF cutoff.
is_constrained.dist_spec | Check if a <dist_spec> is constrained, i.e. has a finite maximum or nonzero CDF cutoff.

## -- L --

LogNormal | Probability distributions

## -- M --

make_conf | Format Credible Intervals
map_prob_change | Categorise the Probability of Change for Rt
max.dist_spec | Returns the maximum of one or more delay distribution
mean.dist_spec | Returns the mean of one or more delay distribution

## -- N --

new_dist_spec | Internal function for generating a 'dist_spec' given parameters and a distribution.
NonParametric | Probability distributions
Normal | Probability distributions

## -- O --

obs_opts | Observation Model Options
opts_list | Forecast optiong

## -- P --

plot.dist_spec | Plot PMF and CDF for a dist_spec object
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.forecast_infections | Plot method for forecast_infections
plot.forecast_secondary | Plot method for forecast_secondary objects
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
print.epinowfit | Print information about an object that has resulted from a model fit.

## -- R --

regional_epinow | Real-time Rt Estimation, Forecasting and Reporting by Region
regional_summary | Regional Summary Output
report_plots | Report plots
report_summary | Provide Summary Statistics for Estimated Infections and Rt
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 --

secondary_opts | Secondary Reports Options
setup_default_logging | Setup Default Logging
setup_future | Set up Future Backend
setup_logging | Setup Logging
simulate_infections | Simulate infections using the renewal equation
simulate_secondary | Simulate secondary observations from primary observations
stan_laplace_opts | Stan Laplace algorithm Options
stan_opts | Stan Options
stan_pathfinder_opts | Stan pathfinder algorithm Options
stan_sampling_opts | Stan Sampling Options
stan_vb_opts | Stan Variational Bayes Options
summary | Summary output from epinow
summary.epinow | Summary output from epinow
summary.estimate_dist | Summarise results from estimate_dist
summary.estimate_infections | Summary output from estimate_infections
summary.estimate_secondary | Summarise results from estimate_secondary
summary.estimate_truncation | Summarise results from estimate_truncation
summary.forecast_infections | Summary output from forecast_infections

## -- T --

trunc_opts | Truncation Distribution Options

## -- U --

update_secondary_args | Update estimate_secondary default priors

## -- W --

Weibull | Probability distributions

## -- misc --

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