Package index • EpiNow2

Estimation + Reporting

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

epinow() stable: Real-time Rt Estimation, Forecasting and Reporting
epinow2_cmdstan_model(): Load and compile an EpiNow2 cmdstanr model
plot(<epinow>) maturing: Plot method for epinow
print(<epinowfit>): Print information about an object that has resulted from a model fit.
regional_epinow() maturing: Real-time Rt Estimation, Forecasting and Reporting by Region
summary(<epinow>) stable: Summary output from epinow

Estimate, Simulate, and Forecast Parameters

Function to estimate, simulate and forecast parameters of interest.

estimate_infections() maturing: Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
forecast_infections() stable: Forecast infections from a given fit and trajectory of the time-varying reproduction number
estimate_secondary() stable: Estimate a Secondary Observation from a Primary Observation
forecast_secondary() experimental: Forecast Secondary Observations Given a Fit from estimate_secondary
estimate_delay() maturing: Estimate a Delay Distribution
estimate_truncation() stable: Estimate Truncation of Observed Data

Specify Arguments

Functions used by estimate_infections

backcalc_opts() stable: Back Calculation Options
delay_opts() stable: Delay Distribution Options
filter_opts() maturing: Filter Options for a Target Region
forecast_opts() stable: Forecast options
gt_opts() generation_time_opts() stable: Generation Time Distribution Options
gp_opts() stable: Approximate Gaussian Process Settings
obs_opts() stable: Observation Model Options
rt_opts() stable: Time-Varying Reproduction Number Options
secondary_opts() stable: Secondary Reports Options
stan_laplace_opts() experimental: Stan Laplace algorithm Options
stan_opts() stable: Stan Options
stan_pathfinder_opts() experimental: Stan pathfinder algorithm Options
stan_sampling_opts() stable: Stan Sampling Options
stan_vb_opts() stable: Stan Variational Bayes Options
trunc_opts() stable: Truncation Distribution Options
opts_list() maturing: Forecast optiong

Preprocess Data

Functions used for preprocessing data

fill_missing() experimental: Fill missing data in a data set to prepare it for use within the package
add_breakpoints(): Add breakpoints to certain dates in a data set.
filter_leading_zeros(): Filter leading zeros from a data set.
apply_zero_threshold(): Convert zero case counts to NA (missing) if the 7-day average is above a threshold.

Regional Analysis

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

regional_summary() maturing: Regional Summary Output
regional_runtimes() maturing: Summarise Regional Runtimes
get_regional_results() stable: Get Combined Regional Results

Summarise Results

Functions for summarising results

summary(<epinow>) stable: Summary output from epinow
summary(<estimate_infections>) stable: Summary output from estimate_infections
summary(<forecast_infections>) stable: Summary output from forecast_infections
backcalc_opts() stable: Back Calculation Options
calc_CrI() stable: Calculate Credible Interval
calc_CrIs() stable: Calculate Credible Intervals
calc_summary_measures() stable: Calculate All Summary Measures
calc_summary_stats() stable: Calculate Summary Statistics
make_conf() stable: Format Credible Intervals
map_prob_change() stable: Categorise the Probability of Change for Rt

Plot Results

Plot generated results

plot(<dist_spec>) experimental: Plot PMF and CDF for a dist_spec object
plot(<epinow>) maturing: Plot method for epinow
plot(<estimate_infections>) maturing: Plot method for estimate_infections
plot(<estimate_secondary>) experimental: Plot method for estimate_secondary
plot(<estimate_truncation>) experimental: Plot method for estimate_truncation
plot(<forecast_infections>) maturing: Plot method for forecast_infections
plot_CrIs() stable: Plot EpiNow2 Credible Intervals
plot_estimates() questioning: Plot Estimates
plot_summary() questioning: Plot a Summary of the Latest Results
report_plots() questioning: Report plots

Report Results

Functions to report results

report_plots() questioning: Report plots
report_summary() questioning: Provide Summary Statistics for Estimated Infections and Rt

Distribution Functions

Functions to define and parameterise distributions

LogNormal() Gamma() Normal() Fixed() NonParametric(): Probability distributions
c(<dist_spec>) experimental: Combines multiple delay distributions for further processing
collapse(<dist_spec>) experimental: Collapse nonparametric distributions in a <dist_spec>
discretise(<dist_spec>) discretize() experimental: Discretise a <dist_spec>
`==`(<dist_spec>) `!=`(<dist_spec>): Compares two delay distributions
fix_parameters(<dist_spec>) experimental: Fix the parameters of a <dist_spec>
is_constrained(<dist_spec>) experimental: Check if a <dist_spec> is constrained, i.e. has a finite maximum or nonzero CDF cutoff.
max(<dist_spec>) experimental: Returns the maximum of one or more delay distribution
mean(<dist_spec>) experimental: Returns the mean of one or more delay distribution
new_dist_spec() experimental: Internal function for generating a dist_spec given parameters and a distribution.
plot(<dist_spec>) experimental: Plot PMF and CDF for a dist_spec object
`+`(<dist_spec>) experimental: Creates a delay distribution as the sum of two other delay distributions.
print(<dist_spec>) experimental: Prints the parameters of one or more delay distributions
bound_dist() experimental: Define bounds of a <dist_spec>
get_parameters() experimental: Get parameters of a parametric distribution
get_pmf() experimental: Get the probability mass function of a nonparametric distribution
get_distribution() experimental: Get the distribution of a <dist_spec>

Fit Delay Distributions

Functions to fit delay distributions

bootstrapped_dist_fit() stable: Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters
dist_fit() stable: Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions

Simulation

Functions to help with simulating data or mapping to reported cases

simulate_infections(): Simulate infections using the renewal equation
simulate_secondary(): Simulate secondary observations from primary observations
convolve_and_scale(): Convolve and scale a time series

Data

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

example_generation_time stable: Example generation time
example_incubation_period stable: Example incubation period
example_reporting_delay stable: Example reporting delay
example_confirmed stable: Example Confirmed Case Data Set
example_truncated stable: Example Case Data Set with Truncation

Data Access

Functions for extracting data from objects or getting data from sources

get_distribution() experimental: Get the distribution of a <dist_spec>
get_parameters() experimental: Get parameters of a parametric distribution
get_pmf() experimental: Get the probability mass function of a nonparametric distribution
get_regional_results() stable: Get Combined Regional Results
get_samples() stable: Get posterior samples from a fitted model
extract_CrIs() stable: Extract Credible Intervals Present
extract_inits() experimental: Generate initial conditions from a Stan fit
extract_samples(): Extract all samples from a stan fit
extract_stan_param() stable: Extract a Parameter Summary from a Stan Object

Data Cleaning

Functions for cleaning data

clean_nowcasts() stable: Clean Nowcasts for a Supplied Date
clean_regions() stable: Clean Regions

Setup

Functions used for setting up functionality

setup_default_logging() questioning: Setup Default Logging
setup_future() stable: Set up Future Backend
setup_logging() questioning: Setup Logging

Utilities

Utility functions

run_region() maturing: Run epinow with Regional Processing Code
expose_stan_fns() stable: Expose internal package stan functions in R
convert_to_logmean() stable: Convert mean and sd to log mean for a log normal distribution
convert_to_logsd() stable: Convert mean and sd to log standard deviation for a log normal distribution
growth_to_R() questioning: Convert Growth Rates to Reproduction numbers.
R_to_growth() questioning: Convert Reproduction Numbers to Growth Rates
update_secondary_args() stable: Update estimate_secondary default priors

Internal

EpiNow2 EpiNow2-package: EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
add_day_of_week(): Adds a day of the week vector
add_horizon(): Add missing values for future dates
allocate_delays() stable: Allocate Delays into Required Stan Format
allocate_empty() stable: Allocate Empty Parameters to a List
apply_default_cdf_cutoff(): Apply default CDF cutoff to a <dist_spec> if it is unconstrained
apply_tolerance() deprecated: Applies a threshold to all nonparametric distributions in a <dist_spec>
check_generation_time() stable: Validate probability distribution for using as generation time
check_reports_valid() stable: Validate data input
check_sparse_pmf_tail(): Check that PMF tail is not sparse
check_stan_delay() stable: Validate probability distribution for passing to stan
construct_output() stable: Construct Output
convert_to_natural() experimental: Internal function for converting parameters to natural parameters.
copy_results_to_latest() questioning: Copy Results From Dated Folder to Latest
create_backcalc_data() stable: Create Back Calculation Data
create_delay_inits(): Create initial conditions for delays
create_future_rt() stable: Construct the Required Future Rt assumption
create_gp_data() stable: Create Gaussian Process Data
create_infection_summary() stable: Create summary output from infection estimation objects
create_initial_conditions() stable: Create Initial Conditions Generating Function
create_obs_model() stable: Create Observation Model Settings
create_rt_data() stable: Create Time-varying Reproduction Number Data
create_shifted_cases() stable: Create Delay Shifted Cases
create_stan_args() stable: Create a List of Stan Arguments
create_stan_data() stable: Create Stan Data Required for estimate_infections
create_stan_delays(): Create delay variables for stan
create_stan_params(): Create parameters for stan
default_fill_missing_obs() deprecated: Temporary function to support the transition to full support of missing data.
discrete_pmf() questioning: Discretised probability mass function
dist_skel() deprecated: Distribution Skeleton
epinow2_rstan_model(): Load an EpiNow2 rstan model.
epinow2_stan_model(): Return a stan model object for the appropriate backend
estimates_by_report_date() questioning: Estimate Cases by Report Date
extract_parameter() stable: Extract Samples for a Parameter from a Stan model
extract_parameter_samples() deprecated: Extract Parameter Samples from a Stan Model
extract_params() experimental: Extract parameter names
extract_single_dist() experimental: Extract a single element of a composite <dist_spec>
extract_static_parameter(): Extract Samples from a Parameter with a Single Dimension
fit_model(): Fit a model using the chosen backend.
fit_model_approximate() maturing: Fit a Stan Model using an approximate method
fit_model_with_nuts() maturing: Fit a Stan Model using the NUTs sampler
fix_dist() deprecated: Remove uncertainty in the parameters of a <dist_spec>
format_fit() stable: Format Posterior Samples
format_samples_with_dates(): Format raw Stan samples with dates and metadata
format_simulation_output() stable: Format Simulation Output from Stan
get_element(): Extracts an element of a <dist_spec>
get_raw_result() stable: Get a Single Raw Result
get_regions() stable: Get Folders with Results
get_regions_with_most_reports() stable: Get Regions with Most Reported Cases
get_seeding_time(): Estimate seeding time from delays and generation time
lapply_func(): Choose a parallel or sequential apply function
lower_bounds() experimental: Get the lower bounds of the parameters of a distribution
make_param(): Internal function to create a parameter list
match_output_arguments() stable: Match User Supplied Arguments with Supported Options
natural_params() experimental: Get the names of the natural parameters of a distribution
ndist(): Calculate the number of distributions in a <dist_spec>
pad_reported_cases(): Pads reported cases with daily initial zeros
process_region() maturing: Process regional estimate
process_regions() stable: Process all Region Estimates
regional_runtimes() maturing: Summarise Regional Runtimes
save_estimate_infections() stable: Save Estimated Infections
save_input() stable: Save Observed Data
sd(<dist_spec>) experimental: Returns the standard deviation of one or more delay distribution
select_plots(): Internal helper function to select plots from those created by report_plots()
set_dt_single_thread(): Set to Single Threading
setup_dt() stable: Convert to Data Table
setup_target_folder() stable: Setup Target Folder for Saving
stable_convolve(): Numerically stable convolution function for two pmf vectors
summarise_key_measures() maturing: Summarise rt and cases
summarise_results() questioning: Summarise Real-time Results
update_horizon() stable: Updates Forecast Horizon Based on Input Data and Target