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
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
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 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
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
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
Functions to report results
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 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
Functions to help with simulating data to evaluate the approach
simulate_cases()
Simulate Cases by Date of Infection, Onset and Report
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
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
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
pull_max_var()
Extract a the Maximum Value of a Variable Based on a Filter