Create Clean Reported Cases — create_clean_reported

Filters leading zeros, completes dates, and applies an optional threshold at which point 0 cases are replaced with a user supplied value (defaults to NA).

Usage

create_clean_reported_cases(
  data,
  filter_leading_zeros = TRUE,
  zero_threshold = Inf,
  fill = NA_integer_,
  add_breakpoints = TRUE
)

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.
filter_leading_zeros: Logical, defaults to TRUE. Should zeros at the start of the time series be filtered out.
zero_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 then the zero is replaced using fill.
fill: Deprecated; zero dates with 7-day averages above the zero_threshold will be skipped in model fitting.
add_breakpoints: Logical, defaults to TRUE. Should a breakpoint column be added to the data frame if it does not exist.

Value

A cleaned data frame of reported cases

Examples

if (FALSE) { # \dontrun{
create_clean_reported_cases(example_confirmed, 7)
} # }