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

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Documentation for package ‘EpiNow2’ version 1.4.0

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

-- A --

add_day_of_week Adds a day of the week vector
adjust_infection_to_report Adjust from Case Counts by Infection Date to Date of Report
allocate_delays Allocate Delays into Required Stan Format
allocate_empty Allocate Empty Parameters to a List

-- B --

backcalc_opts Back Calculation Options
bootstrapped_dist_fit Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters

-- 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
construct_output Construct Output
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
copy_results_to_latest Copy Results From Dated Folder to Latest
create_backcalc_data Create Back Calculation Data
create_clean_reported_cases Create Clean Reported Cases
create_future_rt Construct the Required Future Rt assumption
create_gp_data Create Gaussian Process Data
create_initial_conditions Create Initial Conditions Generating Function
create_obs_model Create Observation Model Settings
create_rt_data Create Time-varying Reproduction Number Data
create_shifted_cases Create Delay Shifted Cases
create_stan_args Create a List of Stan Arguments
create_stan_data Create Stan Data Required for estimate_infections
create_stan_delays Create delay variables for stan

-- D --

delay_opts Delay Distribution Options
dist_fit Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions
dist_skel Distribution Skeleton
dist_spec Specify a distribution.
dist_spec_plus Creates a delay distribution as the sum of two other delay distributions

-- E --

epinow Real-time Rt Estimation, Forecasting and Reporting
estimates_by_report_date Estimate Cases by Report Date
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
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_parameter Extract Samples for a Parameter from a Stan model
extract_parameter_samples Extract Parameter Samples from a Stan Model
extract_stan_param Extract a Parameter Summary from a Stan Object
extract_static_parameter Extract Samples from a Parameter with a Single Dimension

-- F --

filter_opts Filter Options for a Target Region
fit_model_with_nuts Fit a Stan Model using the NUTs sampler
fit_model_with_vb Fit a Stan Model using Variational Inference
forecast_secondary Forecast Secondary Observations Given a Fit from estimate_secondary
format_fit Format Posterior Samples

-- G --

gamma_dist_def Generate a Gamma Distribution Definition Based on Parameter Estimates
generation_times Literature Estimates of Generation Times
generation_time_opts Generation Time Distribution Options
get_dist Get a Literature Distribution
get_generation_time Get a Literature Distribution for the Generation Time
get_incubation_period Get a Literature Distribution for the Incubation Period
get_raw_result Get a Single Raw Result
get_regional_results Get Combined Regional Results
get_regions Get Folders with Results
get_regions_with_most_reports Get Regions with Most Reported Cases
get_seeding_time Estimate seeding time from delays and generation time
gp_opts Approximate Gaussian Process Settings
growth_to_R Convert Growth Rates to Reproduction numbers.

-- I --

incubation_periods Literature Estimates of Incubation Periods
init_cumulative_fit Generate initial conditions by fitting to cumulative cases

-- L --

lognorm_dist_def Generate a Log Normal Distribution Definition Based on Parameter Estimates

-- M --

make_conf Format Credible Intervals
map_prob_change Categorise the Probability of Change for Rt
match_output_arguments Match User Supplied Arguments with Supported Options
mean.dist_spec Returns the mean of one or more delay distribution

-- O --

obs_opts Observation Model Options
opts_list Return an _opts List per Region

-- 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
process_region Process regional estimate
process_regions Process all Region Estimates

-- R --

regional_epinow Real-time Rt Estimation, Forecasting and Reporting by Region
regional_runtimes Summarise Regional Runtimes
regional_summary Regional Summary Output
report_cases Report case counts by date of report
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

-- S --

sample_approx_dist Approximate Sampling a Distribution using Counts
save_estimate_infections Save Estimated Infections
save_input Save Observed Data
secondary_opts Secondary Reports Options
setup_default_logging Setup Default Logging
setup_dt Convert to Data Table
setup_future Set up Future Backend
setup_logging Setup Logging
setup_target_folder Setup Target Folder for Saving
simulate_infections Simulate infections using a given trajectory of the time-varying reproduction number
simulate_secondary Simulate a secondary observation
stan_opts Stan Options
summarise_key_measures Summarise rt and cases
summarise_results Summarise Real-time Results
summary Summary output from epinow
summary.epinow Summary output from epinow
summary.estimate_infections Summary output from estimate_infections

-- T --

trunc_opts Truncation Distribution Options

-- U --

update_horizon Updates Forecast Horizon Based on Input Data and Target
update_list Update a List
update_secondary_args Update estimate_secondary default priors

-- misc --

+.dist_spec Creates a delay distribution as the sum of two other delay distributions