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

Source: R/to_time_series.R
to_time_series.Rd

This function takes observations and the corresponding date vector (time) and converts them into a tsd object, which is a time series data structure that can be used for time series analysis. For count data, supply cases or incidence with given population. For binomial data, supply samples and cases or proportion. Count and binomial inputs are mutually exclusive.

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().

  • proportion will be calculated if supplying cases and samples.

  • cases will be calculated if supplying proportion and samples.

Usage

to_time_series(
  cases = NULL,
  incidence = NULL,
  population = NULL,
  proportion = NULL,
  samples = 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. For binomial data, use samples instead.

proportion

A numeric vector containing binomial proportions in [0, 1] (Will be rescaled to [0, 1] if percentages in (1, 100] are provided). Use with samples for proportional/binomial data.

samples

An integer vector containing number of samples tested. Use with cases or proportion for binomial data.

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)

  • 'proportion': The proportion of cases in the tested samples at the time point for binomial input. (optional)

  • 'samples': The number of samples tested at the time point for binomial input. (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)
)

# Create a `tsd` object with binomial data
tsd_binomial <- to_time_series(
  cases = c(10, 12, 18, 25),
  samples = c(100, 100, 120, 140),
  time = seq(from = as.Date("2023-01-01"), by = "1 week", length.out = 4)
)