Function reference • EpiNow2

Estimation + Reporting

Functions that faciliate end-to-end analysis including imputing cases by infection, estimating Rt and reporting results.

epinow(): Real-time Rt Estimation, Forecasting and Reporting

plot(<epinow>): Plot method for epinow

regional_epinow(): Real-time Rt Estimation, Forecasting and Reporting by Region

summary(<epinow>): Summary output from epinow

Estimate, Simulate, and Forecast Parameters

Function to estimate, simulate and forecast parameters of interest.

estimate_infections(): Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth

simulate_infections(): Simulate infections using a given trajectory of the time-varying reproduction number

estimate_secondary(): Estimate a Secondary Observation from a Primary Observation

forecast_secondary(): Forecast Secondary Observations Given a Fit from estimate_secondary

estimate_delay(): Estimate a Delay Distribution

estimate_truncation(): Estimate Truncation of Observed Data

Internal epinow Functions

Functions used internally by epinow

update_horizon(): Updates Forecast Horizon Based on Input Data and Target

save_estimate_infections(): Save Estimated Infections

save_input(): Save Observed Data

estimates_by_report_date(): Estimate Cases by Report Date

copy_results_to_latest(): Copy Results From Dated Folder to Latest

construct_output(): Construct Output

Internal estimate_infections Functions

Functions used by estimate_infections

backcalc_opts(): Back Calculation Options

delay_opts(): Delay Distribution Options

filter_opts(): Filter Options for a Target Region

generation_time_opts(): Generation Time Distribution Options

gp_opts(): Approximate Gaussian Process Settings

obs_opts(): Observation Model Options

rstan_opts(): Rstan Options

rstan_sampling_opts(): Rstan Sampling Options

rstan_vb_opts(): Rstan Variational Bayes Options

rt_opts(): Time-Varying Reproduction Number Options

secondary_opts(): Secondary Reports Options

stan_opts(): Stan Options

trunc_opts(): Truncation Distribution Options

opts_list(): Return an _opts List per Region

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

allocate_delays(): Allocate Delays into Required Stan Format

allocate_empty(): Allocate Empty Parameters to a List

Model Fitting

Functions for model fitting

fit_model_with_nuts(): Fit a Stan Model using the NUTs sampler

fit_model_with_vb(): Fit a Stan Model using Variational Inference

init_cumulative_fit(): Generate initial conditions by fitting to cumulative cases

Summarise Across Regions

Functions used for summarising across regions (designed for use with regional_epinow)

regional_summary(): Regional Summary Output

regional_runtimes(): Summarise Regional Runtimes

Summarise results

Functions from summarising results

summary(<epinow>): Summary output from epinow

summary(<estimate_infections>): Summary output from estimate_infections

summarise_key_measures(): Summarise rt and cases

summarise_results(): Summarise Real-time Results

backcalc_opts(): Back Calculation Options

calc_CrI(): Calculate Credible Interval

calc_CrIs(): Calculate Credible Intervals

calc_summary_measures(): Calculate All Summary Measures

calc_summary_stats(): Calculate Summary Statistics

create_backcalc_data(): Create Back Calculation Data

process_region(): Process regional estimate

process_regions(): Process all Region Estimates

format_fit(): Format Posterior Samples

make_conf(): Format Credible Intervals

map_prob_change(): Categorise the Probability of Change for Rt

Plot Results

Plot generated results

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

report_plots(): Report plots

Report results

Functions to report results

report_cases(): Report case counts by date of report

report_plots(): Report plots

report_summary(): Provide Summary Statistics for Estimated Infections and Rt

Define, Fit and Parameterise Distributions

Functions to define, fit and parameterise distributions

bootstrapped_dist_fit(): Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters

c(<dist_spec>): Combines multiple delay distributions for further processing

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

fix_dist(): Fix the parameters of a <dist_spec> object

gamma_dist_def(): Generate a Gamma Distribution Definition Based on Parameter Estimates

get_dist(): Get a Literature Distribution

lognorm_dist_def(): Generate a Log Normal Distribution Definition Based on Parameter Estimates

mean(<dist_spec>): Returns the mean of one or more delay distribution

plot(<dist_spec>): Plot PMF and CDF for a dist_spec object

`+`(<dist_spec>): Creates a delay distribution as the sum of two other delay distributions

print(<dist_spec>): Prints the parameters of one or more delay distributions

sample_approx_dist(): Approximate Sampling a Distribution using Counts

Simulate

Functions to help with simulating data or mapping to reported cases

simulate_infections(): Simulate infections using a given trajectory of the time-varying reproduction number

simulate_secondary(): Simulate a secondary observation

adjust_infection_to_report(): Adjust from Case Counts by Infection Date to Date of Report

Data

Package datasets that may be used to parameterise other functions or in examples

example_generation_time: Example generation time

example_incubation_period: Example incubation period

example_reporting_delay: Example reporting delay

example_confirmed: Example Confirmed Case Data Set

generation_times: Literature Estimates of Generation Times

incubation_periods: Literature Estimates of Incubation Periods

Get/Extract Data

Functions for extracting data from objects or getting data from sources

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

setup_target_folder(): Setup Target Folder for Saving

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

Clean Data

Functions for cleaning data

clean_nowcasts(): Clean Nowcasts for a Supplied Date

clean_regions(): Clean Regions

create_clean_reported_cases(): Create Clean Reported Cases

Setup Utilities

Function used for setting up functionality

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

Utilities

Utility functions

match_output_arguments(): Match User Supplied Arguments with Supported Options

run_region(): Run epinow with Regional Processing Code

expose_stan_fns(): Expose internal package stan functions in R

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

growth_to_R(): Convert Growth Rates to Reproduction numbers.

R_to_growth(): Convert Reproduction Numbers to Growth Rates

add_day_of_week(): Adds a day of the week vector

update_secondary_args(): Update estimate_secondary default priors

update_list(): Update a List