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 Parameters

Function to estimate parameters of interest.

estimate_infections()

Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth

forecast_infections()

Forecast Infections and the Time-Varying Reproduction Number

estimate_delay()

Estimate a Delay Distribution

estimate_truncation()

Estimate Truncation of Observed Data

estimate_secondary()

Estimate a Secondary Observation from a Primary Observation

forecast_secondary()

Forecast Secondary Observations Given a Fit from estimate_secondary

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_forecast_infections()

Save Forecast 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

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

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(<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

dist_fit()

Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions

dist_skel()

Distribution Skeleton

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

sample_approx_dist()

Approximate Sampling a Distribution using Counts

tune_inv_gamma()

Tune an Inverse Gamma to Achieve the Target Truncation

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_cases()

Simulate Cases by Date of Infection, Onset and Report

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

generation_times

Literature Estimates of Generation Times

incubation_periods

Literature Estimates of Incubation Periods

example_confirmed

Example Confirmed Case Data Set

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

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

Map results

Optional mapping functions (requires additional dependencies)

global_map()

Generate a global map for a single variable.

country_map()

Generate a country map for a single variable.

theme_map()

Custom Map Theme

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

update_list()

Update a List

add_day_of_week()

Adds a day of the week vector