+.dist_spec             Creates a delay distribution as the sum of two
                        other delay distributions.
==.dist_spec            Compares two delay distributions
Distributions           Probability distributions
R_to_growth             Convert Reproduction Numbers to Growth Rates
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.
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.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>
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
delay_opts              Delay Distribution Options
discretise              Discretise a <dist_spec>
dist_fit                Fit an Integer Adjusted Exponential, Gamma or
                        Lognormal distributions
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_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
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
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
fix_parameters          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
get_distribution        Get the distribution of a <dist_spec>
get_parameters          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_regional_results    Get Combined Regional Results
get_samples             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
is_constrained          Check if a <dist_spec> is constrained, i.e. has
                        a finite maximum or nonzero CDF cutoff.
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
new_dist_spec           Internal function for generating a 'dist_spec'
                        given parameters and a distribution.
obs_opts                Observation Model Options
opts_list               Forecast optiong
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.
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
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.epinow          Summary output from epinow
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
trunc_opts              Truncation Distribution Options
update_secondary_args   Update estimate_secondary default priors
