enw_linelist_to_incidence: Convert a Line List to Aggregate Counts (Incidence)

In seabbs/epinowcast: Flexible Hierarchical Nowcasting

Convert a Line List to Aggregate Counts (Incidence)

Description

This function takes a line list (i.e. tabular data where each row represents a case) and aggregates to a count (new_confirm) of cases by user-specified reference_dates and report_dates. This is enables the use of enw_preprocess_data() and other epinowcast() preprocessing functions.

Usage

enw_linelist_to_incidence(
  linelist,
  reference_date = "reference_date",
  report_date = "report_date",
  by = NULL,
  max_delay,
  completion_beyond_max_report = FALSE,
  copy = TRUE
)

Arguments

linelist	An object coercible to a data.table (such as a data.frame) where each row represents a case. Must contain at least two date variables or variables that can be coerced to dates.
reference_date	A date or a variable that can be coerced to a date that represents the date of interest for the case. For example, if the reference_date is the date of symptom onset then the new_confirm will be the number of new cases reported (based on report_date) on each day that had onset on that day. The default is "reference_date".
report_date	A date or a variable that can be coerced to a date that represents the date the case was reported. The default is "report_date".
by	A character vector of variables to also aggregate by (i.e. as well as using the reference_date and report_date). If not supplied then the function will aggregate by just the reference_date and report_date.
max_delay	The maximum number of days between the reference_date and the report_date. If not supplied then the function will use the maximum number of days between the reference_date and the report_date in the linelist. If the max_delay is less than the maximum number of days between the reference_date and the report_date in the linelist then the function will use this value instead and inform the user.
completion_beyond_max_report	Logical, should entries be completed beyond the maximum date found in the data? Default: FALSE
copy	Should obs be copied (default) or modified in place?

Value

A data.table with the following variables: reference_date, report_date, new_confirm, confirm, delay, and any variables specified in by.

See Also

Data converters enw_add_cumulative(), enw_add_incidence(), enw_aggregate_cumulative(), enw_cumulative_to_incidence(), enw_incidence_to_cumulative(), enw_incidence_to_linelist()

Examples

linelist <- data.frame(
  onset_date = as.Date(c("2021-01-02", "2021-01-03", "2021-01-02")),
  report_date = as.Date(c("2021-01-03", "2021-01-05", "2021-01-04"))
)
enw_linelist_to_incidence(linelist, reference_date = "onset_date")

# Specify a custom maximum delay and allow completion beyond the maximum
# observed delay
enw_linelist_to_incidence(
 linelist, reference_date = "onset_date", max_delay = 5,
 completion_beyond_max_report = TRUE
)

seabbs/epinowcast documentation built on Feb. 3, 2025, 9:56 p.m.