## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
#  # alert if all values are NA
#  ars <- alert_rules(alert_missing(extent_type = "all"))
#  
#  # alert if there are 10 or more missing values in total
#  # or if the last 3 or more values are missing
#  # or if 5 or more values in a row are missing
#  ars <- alert_rules(
#    alert_missing(extent_type = "any", extent_value = 10),
#    alert_missing(extent_type = "last", extent_value = 3),
#    alert_missing(extent_type = "consecutive", extent_value = 5)
#  )

## ----eval=FALSE---------------------------------------------------------------
#  # alert if the mean of last 3 values is more than 20% higher than
#  # the mean of the preceding 12 values
#  ars <- alert_rules(
#    alert_difference_above_perc(
#      current_period = 1:3,
#      previous_period = 4:15,
#      rule_value = 20
#    )
#  )

## ----eval=FALSE---------------------------------------------------------------
#  ars <- alert_rules(
#    alert_custom(
#      short_name = "my_rule_combo",
#      description = "Over 3 missing values and max value is > 10",
#      function_call = quote(
#        sum(is.na(value)) > 3 && max(value, na.rm = TRUE) > 10
#      )
#    ),
#    alert_custom(
#      short_name = "my_rule_doubled",
#      description = "Last value is over double the first value",
#      function_call = quote(
#        rev(value)[1] > 2 * value[1]
#      )
#    )
#  )

## -----------------------------------------------------------------------------
library(mantis)

data("example_prescription_numbers")

## ----eval=FALSE---------------------------------------------------------------
#  mantis_report(
#    df = example_prescription_numbers,
#    file = "example_prescription_numbers_interactive.html",
#    inputspec = inputspec(
#      timepoint_col = "PrescriptionDate",
#      item_cols = c("Antibiotic", "Spectrum", "Location"),
#      value_col = "NumberOfPrescriptions",
#      tab_col = "Location"
#    ),
#    outputspec = outputspec_interactive(
#      sync_axis_range = FALSE
#    ),
#    report_title = "mantis report",
#    dataset_description = "Antibiotic prescriptions by site",
#    show_progress = TRUE
#  )

## ----eval=FALSE---------------------------------------------------------------
#  ars <- alert_rules(
#    alert_missing(extent_type = "any", extent_value = 1),
#    alert_custom(
#      short_name = "my_rule_doubled",
#      description = "Last 7 values are over double the first 7 values",
#      function_call = quote(
#        mean(rev(value)[1:7], na.rm = TRUE) > 2 * (mean(value[1:7], na.rm = TRUE))
#      )
#    )
#  )
#  
#  # create a new report
#  mantis_report(
#    df = example_prescription_numbers,
#    file = "example_prescription_numbers_interactive_alerts.html",
#    inputspec = inputspec(
#      timepoint_col = "PrescriptionDate",
#      item_cols = c("Antibiotic", "Spectrum", "Location"),
#      value_col = "NumberOfPrescriptions",
#      tab_col = "Location"
#    ),
#    outputspec = outputspec_interactive(
#      sync_axis_range = FALSE
#    ),
#    alertspec = alertspec(
#      alert_rules = ars,
#      show_tab_results = c("FAIL", "NA")
#    ),
#    report_title = "mantis report with alerts",
#    dataset_description = "Antibiotic prescriptions by site",
#    show_progress = TRUE
#  )

## ----eval=FALSE---------------------------------------------------------------
#  ars_restricted <- alert_rules(
#    alert_missing(extent_type = "any", extent_value = 1),
#    alert_custom(
#      short_name = "my_rule_doubled",
#      description = "Last 7 values are over double the first 7 values",
#      function_call = quote(
#        mean(rev(value)[1:7], na.rm = TRUE) > 2 * (mean(value[1:7], na.rm = TRUE))
#      ),
#      items = list("Spectrum" = c("Broad"))
#    )
#  )
#  
#  # create a new report
#  mantis_report(
#    df = example_prescription_numbers,
#    file = "example_prescription_numbers_interactive_alerts_restricted.html",
#    inputspec = inputspec(
#      timepoint_col = "PrescriptionDate",
#      item_cols = c("Antibiotic", "Spectrum", "Location"),
#      value_col = "NumberOfPrescriptions",
#      tab_col = "Location"
#    ),
#    outputspec = outputspec_interactive(
#      sync_axis_range = FALSE
#    ),
#    alertspec = alertspec(
#      alert_rules = ars_restricted
#    ),
#    report_title = "mantis report with alerts",
#    dataset_description = "Antibiotic prescriptions by site",
#    show_progress = TRUE
#  )