to_time_series: Create a tibble-like 'tsd' (time-series data) object from...

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

Create a tibble-like tsd (time-series data) object from time series data and corresponding dates.

Description

This function takes cases and the corresponding date vector (time) and converts it into a tsd object, which is a time series data structure that can be used for time series analysis. If incidence is added, it will be used as observation in all future use of the aedseo package on the defined tsd object.

Options:

• incidence can be calculated if also supplying cases, population, and incidence_denominator.

• cases can be calculated if also supplying incidence, population and incidence_denominator.

• If background population changes during the time series, it is used to adjust the growth rate in seasonal_onset().

Usage

to_time_series(
  cases = NULL,
  incidence = NULL,
  population = NULL,
  incidence_denominator = if (is.null(population)) NA_real_ else 1e+05,
  time,
  time_interval = c("weeks", "days", "months")
)

Arguments

cases	An integer vector containing the time series cases.
incidence	A numeric vector containing the time series incidences. With the given incidence_denominator.
population	An integer vector containing the time series background population.
incidence_denominator	An integer >= 1, specifying the observations per incidence-denominator.
time	A date vector containing the corresponding dates.
time_interval	A character vector specifying the time interval. Choose between 'days', 'weeks', or 'months'.

Value

A tsd object containing:

• 'time': The time point for the corresponding data.

• 'cases': The number of cases at the time point.

• 'incidence': The incidence per incidence_denominator at the time point. (optional)

• 'population': The background population for the cases at the time point. (optional)

Examples

# Create a `tsd` object with only cases
tsd_cases <- to_time_series(
  cases = c(10, 15, 20, 18),
  time = seq(from = as.Date("2023-01-01"), by = "1 week", length.out = 4)
)

# Create a `tsd` object with incidence from cases, population and default incidence_denominator
tsd_calculate_incidence <- to_time_series(
  cases = c(100, 120, 130, 150),
  time = seq(from = as.Date("2023-01-01"), by = "1 week", length.out = 4),
  population = c(3000000, 3000000, 3000000, 3000000)
)

# Create a `tsd` object with cases from incidence, population and default incidence_denominator
tsd_calculate_cases <- to_time_series(
  incidence = c(5, 7.8, 8, 8.5),
  time = seq(from = as.Date("2023-01-01"), by = "1 week", length.out = 4),
  population = c(3000000, 3000000, 3000000, 3000000)
)

aedseo documentation built on Nov. 18, 2025, 1:07 a.m.