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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
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

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

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