merge_outputs: Merge multiple module outputs into tibble

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

Merge multiple module outputs into tibble

Description

Output tibble from list of unsynced module outputs, with an optional date column. The optional ref_date argument is the starting date of an input with offset 0. In general, this will be the date corresponding to the first entry in the original incidence data. If a reference date is provided with ref_date, a date column is appended to the tibble, with sequential dates generated with the time step specified by the time_step parameter.

Usage

merge_outputs(
  output_list,
  ref_date = NULL,
  time_step = "day",
  include_index = is.null(ref_date),
  index_col = "idx"
)

Arguments

output_list	named list of module output objects.
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)
include_index	boolean. Include an index column in output?
index_col	string. If include_index is TRUE, an index column named index_col is added to the output.

Value

tibble

Examples

shape_incubation = 3.2
scale_incubation = 1.3
delay_incubation <- list(name="gamma", shape = shape_incubation, scale = scale_incubation)

smoothed_incidence <- smooth_incidence(HK_incidence_data$onset_incidence)
deconvolved_incidence <- deconvolve_incidence(
  smoothed_incidence,
  delay = delay_incubation
)

## Basic usage of merge_outputs

merged_incidence_1 <- merge_outputs(
  list("smoothed symptom onset" = smoothed_incidence,
       "deconvolved symptom onset" = deconvolved_incidence)
)


## Advanced usage of merge_outputs

merged_incidence_2 <- merge_outputs(
  list("smoothed symptom onset" = smoothed_incidence,
       "deconvolved symptom onset" = deconvolved_incidence),
  ref_date = HK_incidence_data$date[1],
  include_index = TRUE,
  index_col = "index"
)

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