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

Documentation for package ‘EpiNow2’ version 1.7.1

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-- 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.

-- 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
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_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

-- 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 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.
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 --

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	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

-- 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_infections	Summary output from estimate_infections

-- T --

Truncation Distribution Options

-- U --

Update estimate_secondary default priors

-- 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