make_tibble_from_output: Convert module output object into tibble

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

Convert module output object into tibble

Description

Convert module output object into tibble

Usage

make_tibble_from_output(
  output,
  output_name = "value",
  index_col = "idx",
  ref_date = NULL,
  time_step = "day"
)

Arguments

output	Module input object. List with two elements: A numeric vector named values: the incidence recorded on consecutive time steps. An integer named index_offset: the offset, counted in number of time steps, by which the first value in values is shifted compared to a reference time step This parameter allows one to keep track of the date of the first value in values without needing to carry a date column around. A positive offset means values are delayed in the future compared to the reference values. A negative offset means the opposite.
output_name	string. Name to be given to the values column
index_col	string. Name of the index column included in the output. If a ref_date is passed to the function, the result will contain a date column instead. Even so, a value must be given to this argument for internal steps.
ref_date	Date. Optional. Date of the first data entry in incidence_data
time_step	string. Time between two consecutive incidence datapoints. "day", "2 days", "week", "year"... (see seq.Date for details)

Value

tibble

Examples

## Basic usage of make_tibble_from_output

smoothed_incidence <- smooth_incidence(
  incidence_data = HK_incidence_data$case_incidence,
  smoothing_method = "LOESS"
)

smoothed_incidence_tibble_1 <- make_tibble_from_output(smoothed_incidence)


## Advanced usage of make_tibble_from_output

smoothed_incidence_tibble_2 <- make_tibble_from_output(
  output = smoothed_incidence,
  output_name = "incidence",
  ref_date = HK_incidence_data$date[1]
)

covid-19-Re/estimateR documentation built on Sept. 14, 2024, 5:49 a.m.