Define, Fit and Parameterise Distributions

Functions to define, fit and parameterise distributions

dist_fit()

Fit an integer adjusted exponential or gamma distribution

dist_skel()

Distribution Skeleton

gamma_dist_def()

Generate a Gamma Distribution Definition Based on Parameter Estimates

get_dist_def()

Get a Parameters that Define a Discrete Distribution

lognorm_dist_def()

Generate a Log Normal Distribution Definition Based on Parameter Estimates

sample_approx_dist()

Approximate Sampling a Distribution using Counts

sample_delay()

Sample Onset Dates for Cases missing them

Pipelines

Functions that wrap multiple package components.

nowcast_pipeline()

Impute Cases Date of Infection

epi_measures_pipeline()

Estimate time-varying measures and forecast

rt_pipeline()

Real-time Pipeline

regional_rt_pipeline()

Regional Realtime Pipeline

Estimate Parameters

Function to estimate time-varying parameters of interest.

estimate_R0()

Estimate the time varying R0 - using EpiEstim

estimate_doubling_time()

Estimate the doubling time

estimate_little_r()

Estimate r

estimate_r_in_window()

Estimate r in a set time window

estimate_time_varying_r()

Estimate time varying r

growth_to_R()

Convert Growth Rates to Reproduction numbers.

R_to_growth()

Convert Reproduction Numbers to Growth Rates

Adjust Case Counts

Adjust case counts for right truncation and from date of report to infection

rbinom_size()

Draw with an offset from a negative binomial distribution

adjust_for_truncation()

Adjust Case Counts for Truncation

adjust_infection_to_report()

Adjust from Case Counts by Infection Date to Date of Report

Linelist Tools

Tools for manipulating linelists

generate_pseudo_linelist()

Generate a sample linelist from the observed linelist and sampled linelists

linelist_from_case_counts()

Sample a linelist from case counts and a reporting delay distribution

split_linelist_by_day()

Convert a linelist into a nested `data.table`` of linelists by day

Summarise results

Summarise results

regional_summary()

Generate Regional Summary Output

summarise_cast()

Summarise a nowcast

summarise_results()

Summarise Realtime Results

summarise_to_csv()

Summarise rt and cases as a csv

Report results

Functions to report results

adjust_infection_to_report()

Adjust from Case Counts by Infection Date to Date of Report

report_cases()

Report case counts by date of report

report_littler()

Report Rate of Growth Estimates

report_nowcast()

Report Case Nowcast Estimates

report_reff()

Report Effective Reproduction Number Estimates

report_summary()

Provide Summary Statistics on an Rt Pipeline

Plot results

Plot generated results

plot_confidence()

Plot a Time Series with Confidence.

plot_forecast()

Add a Forecast to a Plot

plot_grid()

Plot a Grid of Plots

plot_pipeline()

Plot Pipeline Results

plot_summary()

Plot a Summary of the Latest Results

Simulate

Functions to help with simulating data to evaluate the approach

simulate_cases()

Simulate Cases by Date of Infection, Onset and Report

Data

Package datasets that are used as defaults by other functions.

covid_incubation_period

Covid Incubation Period

covid_serial_intervals

Covid Generation Serial Intervals

covid_generation_times

Covid Generation Time Estimates

covid_generation_times_summary

Covid Generation Time Estimates - Summary

Map results

Optional mapping functions (requires additional dependencies)

country_map()

Generate a country map for a single variable.

global_map()

Generate a global map for a single variable.

map_prob_change()

Categorise the Probability of Change for Rt

theme_map()

Custom Map Theme

Utilities

Utility functions

get_regions()

Get Folders with Nowcast Results

load_nowcast_result()

Load nowcast results

get_timeseries()

Get Timeseries from EpiNow

clean_nowcasts()

Clean Nowcasts for a Supplied Date

add_dates()

Add Dates from Daata

make_conf()

Format Credible Intervals

map_prob_change()

Categorise the Probability of Change for Rt

pull_max_var()

Extract a the Maximum Value of a Variable Based on a Filter