apply_zero_threshold: Convert zero case counts to 'NA' (missing) if the 7-day...

In epiforecasts/EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Convert zero case counts to NA (missing) if the 7-day average is above a threshold.

Description

This function aims to detect spurious zeroes by comparing the 7-day average of the case counts to a threshold. If the 7-day average is above the threshold, the zero case count is replaced with NA.

Usage

apply_zero_threshold(data, threshold = Inf, obs_column = "confirm")

Arguments

data	A ⁠<data.frame>⁠ of confirmed cases (confirm) by date (date). confirm must be numeric and date must be in date format. Optionally this can also have a logical accumulate column which indicates whether data should be added to the next data point. This is useful when modelling e.g. weekly incidence data. See also the fill_missing() function which helps add the accumulate column with the desired properties when dealing with non-daily data. If any accumulation is done this happens after truncation as specified by the truncation argument.
threshold	Numeric, defaults to Inf. Indicates if detected zero cases are meaningful by using a threshold number of cases based on the 7-day average. If the average is above this threshold at the time of a zero observation count then the zero is replaced with a missing (NA) count and thus ignored in the likelihood.
obs_column	Character (default: "confirm"). If given, only the column specified here will be used for checking missingness. This is useful if using a data set that has multiple columns of hwich one of them corresponds to observations that are to be processed here.

Value

A data.table with the zero threshold applied.

epiforecasts/EpiNow2 documentation built on Dec. 20, 2024, 10:12 p.m.