Calculate low case count diagnostic flag

The diagnostic flag is TRUE if either of the last two weeks of the dataset have fewer than an aggregate X cases per week. See the low_case_count_threshold parameter for what the value of X is. This aggregation excludes the count from confirmed outliers, which have been set to NA in the data.

Usage

low_case_count_diagnostic(df, low_count_threshold)

Arguments

df

A dataframe as returned by read_data(). The dataframe must include columns such as reference_date (a date vector) and confirm (the number of confirmed cases per day).

low_count_threshold

an integer that determines cutoff for determining low_case_count flag. If the jurisdiction has less than X ED visist for the respective pathogen, it will be considered as having too few cases and later on in post-processing the Rt estimate and growth category will be edited to NA and "Not Estimated", respectively

Value

A logical value (TRUE or FALSE) indicating whether either of the last two weeks in the dataset had fewer than 10 cases per week.

Details

This function assumes that the df input dataset has been "completed": that any implicit missingness has been made explicit.

See also

Other diagnostics: extract_diagnostics(), low_case_count_threshold()