inst/doc/multiple_waves.R

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

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, warning=FALSE, message=FALSE--------------------------------------
library(aedseo)

## ----dpi=300------------------------------------------------------------------
set.seed(222)
tsd_data_monthly <- generate_seasonal_data(
  years = 14,
  phase = 3,
  start_date = as.Date("2020-05-18"),
  noise_overdispersion = 5,
  time_interval = "months"
)

tsd_data <- to_time_series(
  cases = tsd_data_monthly$cases,
  time = seq.Date(
    from = as.Date("2020-05-18"),
    by = "week",
    length.out = length(tsd_data_monthly$cases)
  )
) |>
  dplyr::filter(time < as.Date("2023-05-22"))
plot(tsd_data)

## -----------------------------------------------------------------------------
disease_threshold <- estimate_disease_threshold(tsd_data)

## -----------------------------------------------------------------------------
multiple_waves <- combined_seasonal_output(
  tsd_data,
  disease_threshold = disease_threshold$disease_threshold,
  multiple_waves = TRUE,
  burden_level_decrease = "low",
  steps_with_decrease = 2
)

## ----echo = FALSE, dpi=300----------------------------------------------------
plot(multiple_waves)