Dynamically generate a table containing alert results for an rmd chunk

Add mantis alert results to an existing rmarkdown report. The function writes directly to the chunk using side-effects, so chunk options must contain results = 'asis'.

Usage

bespoke_rmd_alert_results(
  df,
  inputspec,
  alert_rules,
  filter_results = c("PASS", "FAIL", "NA"),
  timepoint_limits = c(NA, NA),
  fill_with_zero = FALSE,
  tab_name = NULL,
  tab_level = 1
)

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. Any "tab" column specification will be ignored.
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
fill_with_zero: Logical. Replace any missing or NA values with 0? Useful when value_col is a record count
tab_name: Character string to appear on the tab label. If omitted or NULL, only the content (and not the parent tab) will be created.
tab_level: integer specifying the nesting level of the tab. If tab_name is specified, a value of 1 generates a tab at rmd level "##". If tab_name is not specified, this is ignored.

Value

(invisibly) the supplied df

Examples

if (FALSE) { # \dontrun{

# put this inside a chunk in the rmd file,
# with chunk option `results = 'asis'`
mantis::bespoke_rmd_alert_results(
  df = mantis::example_prescription_numbers,
  inputspec = mantis::inputspec(
    timepoint_col = "PrescriptionDate",
    item_cols = c("Location", "Antibiotic"),
    value_col = "NumberOfPrescriptions",
    tab_col = "Location"
  ),
  alert_rules = alert_rules(
    alert_missing(extent_type = "any", extent_value = 1),
    alert_equals(extent_type = "all", rule_value = 0)
  ),
  filter_results = c("FAIL", "NA"),
  fill_with_zero = FALSE,
  tab_name = "Failed alerts",
  tab_level = 1
)
} # }