+.dist_spec             Creates a delay distribution as the sum of two
                        other delay distributions.
Distributions           Probability distributions
R_to_growth             Convert Reproduction Numbers to Growth Rates
apply_tolerance         Applies a threshold to all nonparametric
                        distributions in a <dist_spec>
backcalc_opts           Back Calculation Options
bootstrapped_dist_fit   Fit a Subsampled Bootstrap to Integer Values
                        and Summarise Distribution Parameters
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
dist_skel               Distribution Skeleton
epinow                  Real-time Rt Estimation, Forecasting and
                        Reporting
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
filter_opts             Filter Options for a Target Region
fix_dist                Fix the parameters of a <dist_spec>
forecast_infections     Forecast infections from a given fit and
                        trajectory of the time-varying reproduction
                        number
forecast_secondary      Forecast Secondary Observations Given a Fit
                        from estimate_secondary
generation_time_opts    Generation Time Distribution Options
generation_times        Literature Estimates of Generation Times
get_distribution        Get the distribution of a 'dist_spec()'
get_parameters          Get parameters of a parametric distribution
get_pmf                 Get the probability mass function of a
                        nonparametric distribution
get_regional_results    Get Combined Regional Results
gp_opts                 Approximate Gaussian Process Settings
growth_to_R             Convert Growth Rates to Reproduction numbers.
incubation_periods      Literature Estimates of Incubation Periods
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               Return an _opts List per Region
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
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
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
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
trunc_opts              Truncation Distribution Options
update_secondary_args   Update estimate_secondary default priors
