Generate a data frame containing alert results

Test the time series for a set of conditions without generating an html report. This can be useful for incorporation into a pipeline.

Usage

mantis_alerts(
  df,
  inputspec,
  alert_rules,
  filter_results = c("PASS", "FAIL", "NA"),
  timepoint_limits = c(NA, NA),
  fill_with_zero = FALSE
)

Arguments

df: A data frame containing multiple time series in long format. See Details.
inputspec: inputspec() object specifying which columns in the supplied df represent the "timepoint", "item", and "value" for the time series.
alert_rules: alert_rules() object specifying conditions to test
filter_results: Only return rows where the alert result is in this vector of values. Alert results can be "PASS", "FAIL", or "NA".
timepoint_limits: Set start and end dates for time period to include. Defaults to min/max of timepoint_col. Can be either Date values or NAs.
fill_with_zero: Logical. Replace any missing or NA values with 0? Useful when value_col is a record count.

Value

tibble

Details

The supplied data frame should contain multiple time series in long format, i.e.:

one "timepoint" (date/posixt) column which will be used for the x-axes. Values should follow a regular pattern, e.g. daily or monthly, but do not have to be consecutive.
one or more "item" (character) columns containing categorical values identifying distinct time series.
one "value" (numeric) column containing the time series values which will be used for the y-axes.

The inputspec parameter maps the data frame columns to the above.

Examples

alert_results <- mantis_alerts(
  example_prescription_numbers,
  inputspec = inputspec(
    timepoint_col = "PrescriptionDate",
    item_cols = c("Antibiotic", "Location"),
    value_col = "NumberOfPrescriptions"
  ),
  alert_rules = alert_rules(
    alert_missing(extent_type = "any", extent_value = 1),
    alert_equals(extent_type = "all", rule_value = 0)
  )
)