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

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

## Documentation for package ‘EpiNow2’ version 1.5.2

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

## Help Pages

+.dist_spec | Creates a delay distribution as the sum of two other delay distributions.
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>
discretize | Discretise a <dist_spec>
Distributions | Probability distributions
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
Fixed | Probability distributions
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
Gamma | Probability distributions
generation_times | Literature Estimates of Generation Times
generation_time_opts | Generation Time Distribution Options
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
LogNormal | Probability distributions
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.
NonParametric | Probability distributions
Normal | Probability distributions
obs_opts | Observation Model Options
opts_list | Return an _opts List per Region
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
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
R_to_growth | Convert Reproduction Numbers to Growth Rates
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_infections | Summary output from estimate_infections
trunc_opts | Truncation Distribution Options
update_secondary_args | Update estimate_secondary default priors