historical_summary: Summarises estimates like seasonal peak and onset from all...

In aedseo: Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

Summarises estimates like seasonal peak and onset from all available seasons

Description

This function summarises peak timing and seasonal onset from estimates in a tsd_onset object. This can be useful for investigating if the current season falls within estimates from previous seasons or if it is very distinct from previous seasons.

Uses data from a tsd_onset object (output from seasonal_onset()).

seasonal_onset() has to be run with arguments;

• disease_threshold

• season_start

• season_end

• only_current_season = FALSE

Usage

historical_summary(onset_output)

Arguments

onset_output

A tsd_onset object returned from seasonal_onset().

Value

An object of class historical_summary, containing:

• Usual time to seasonal peak (weeks after onset)

• The week in which the peak usually falls

• Usual peak intensity

• The week in which the onset usually falls

• Usual onset intensity and growth rate estimates

Examples

# Generate simulated data of seasonal waves
sim_data <- generate_seasonal_data(
  years = 5,
  start_date = as.Date("2022-05-26"),
  trend_rate = 1.002,
  noise_overdispersion = 1.1
)

# Estimate seasonal onset
tsd_onset <- seasonal_onset(
  tsd = sim_data,
  disease_threshold = 20,
  family = "quasipoisson",
  season_start = 21,
  season_end = 20,
  only_current_season = FALSE
)

# Get historical summary
historical_summary(tsd_onset)

aedseo documentation built on April 12, 2025, 1:35 a.m.