evalALERT: Cross-validating ALERT output under a rule

In nickreich/ALERT: The Above Local Elevated Respiratory illness Threshold (ALERT) Algorithm

Description

The evalALERT function uses the ALERT algorithm to test a rule (either minPercent or maxDuration) on hospital influenza data. For each season in the dataset, createALERT finds an optimal ALERT threshold when leaving that year out. Then applyALERT tests that threshold in that year. The metrics are saved and summarized.

Usage

evalALERT(data, minPercent = NULL, maxDuration = NULL, firstMonth = 9,
  lag = 7, minWeeks = 8, allThresholds = FALSE, k = 0,
  target.pct = NULL, caseColumn = "Cases")

Arguments

data	the historical data to use in the analysis. A data frame with a 'Date' column (must be Date objects) and a 'Cases' column.
minPercent	specify the minimum percent of cases to be captured at least 50% of the time by ALERT. This enables automated threshold selection.
maxDuration	specify the maximum number of weeks to be captured at least 50% of the time by ALERT. This enables automated threshold selection.
firstMonth	month number which is counted as the first month of the 'flu year'
lag	lag time between report date and action taken
minWeeks	minimum number of weeks to be in ALERT
allThresholds	if TRUE, all integer threshold values between the 10th and 50th percentile are examined. If FALSE, only the 10th, 20th, 30th, 40th, and 50th percentiles are examined.
k	the number of weeks around the peak to evaluate ALERT coverage for
target.pct	the percentage of cases the user is targeting during the ALERT period when
caseColumn	the name of the column with the case counts in it. Defaults to 'Cases' testing maxDuration (optional)

Value

Returns a table with the following columns:

season	each flu season in the data that was able to be evaluated for the given rule, with the final row reserved for summary statistics
threshold	the minimum threshold number of cases needed to begin the ALERT period
tot.cases	total number of cases for the season
duration	duration of the ALERT period
ALERT.cases	total number of cases in the ALERT period
ALERT.cases.pct	fraction of cases in the ALERT period
peak.captured	1 if peak was captured, 0 otherwise
peak.ext.captured	1 if peak +/- k weeks captured, 0 otherwise
low.weeks.incl	the number of weeks included in the ALERT period with counts less than threshold
duration.diff	if target.pct specified, the difference between the duration of the ALERT period and the duration of the shortest period needed to capture target.pct using postcastALERT.

Each row in the table represents a season from the data. The final row outputs summary statistics: the median of threshold, tot.cases, duration, ALERT.cases, and ALERT.cases.pct and the mean of peak.captured, peak.ext.captured, low.weeks.incl, and duration.diff.

Author(s)

Nicholas G Reich and Stephen A Lauer

See Also

robustALERT cross-validates ALERT output under a set of rules

Examples

## find the highest threshold captures at least 85% half of the time
data(fluData)
evalALERT(minPercent=.85, data=fluData, k=2)

## find the lowest threshold that has a median duration of less than 12 weeks
evalALERT(maxDuration=12, data=fluData, k=2)

nickreich/ALERT documentation built on Jan. 8, 2020, 5:25 p.m.