enw_simulate_missing_reference: Simulate observations with a missing reference date.

In seabbs/epinowcast: Flexible Hierarchical Nowcasting

Simulate observations with a missing reference date.

Description

A simple binomial simulator of missing data by reference date using simulated or observed data as an input. This function may be used to validate missing data models, as part of examples and case studies, or to explore the implications of missing data for your use case.

Usage

enw_simulate_missing_reference(obs, proportion = 0.2, by = NULL)

Arguments

obs	A data.frame containing at least the following variables: ⁠reference date⁠ (index date of interest), report_date (report date for observations), and confirm (cumulative observations by reference and report date).
proportion	Numeric, the proportion of observations that are missing a reference date, indexed by reference date. Currently only a fixed proportion are supported and this defaults to 0.2.
by	A character vector describing the stratification of observations. This defaults to no grouping. This should be used when modelling multiple time series in order to identify them for downstream modelling

Value

A data.table of the same format as the input but with a simulated proportion of observations now having a missing reference date.

Examples

# Load and filter germany hospitalisations
nat_germany_hosp <- subset(
  germany_covid19_hosp, location == "DE" & age_group == "00+"
)
nat_germany_hosp <- enw_filter_report_dates(
  nat_germany_hosp,
  latest_date = "2021-08-01"
)

# Make sure observations are complete
nat_germany_hosp <- enw_complete_dates(
  nat_germany_hosp,
  by = c("location", "age_group"), missing_reference = FALSE
)

# Simulate
enw_simulate_missing_reference(
  nat_germany_hosp,
  proportion = 0.35, by = c("location", "age_group")
)

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