robustALERT: Cross-validating ALERT over a set of rules.

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

Description

The robustALERT function finds the optimal threshold for starting an ALERT season for a vector of rules. For each rule specified, evalALERT tests the rule against every flu season for the given data and outputs summary statistics. robustALERT aggregates these statistics together for easy comparison. This function can be used to validate the results from createALERT.

Usage

robustALERT(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	value or vector that specifies the minimum percent of cases to be captured at least 50% of the time by ALERT. This enables automated threshold selection.
maxDuration	value or vector that specifies the maximum number of weeks to be captured at least 50% of the time by ALERT. This enables automated threshold selection.
firstMonth	firstMonth month number which is counted as the first month of the 'flu year'
lag	lag time in days between date of cases 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	if not 0, the number of weeks around the peak to evaluate ALERT coverage for
target.pct	can specify the percentage of cases the user is targeting during the ALERT period when testing maxDuration (optional)
caseColumn	the name of the column with the case counts in it. Defaults to 'Cases'

Value

A table of the median threshold and ALERT results determined by each rule with evalALERT with the following columns:

rule	each rule that was specified by the user, either by minPercent or maxDuration
threshold	the median threshold number of cases needed to begin a sufficient ALERT period
duration	the median duration of the ALERT period
ALERT.cases	the median number of cases in the ALERT period
ALERT.cases.pct	the median fraction of cases in the ALERT period
peak.captured	the fraction of the time the peak was captured
peak.ext.captured	the fraction of the time the peak +/- k weeks was captured
low.weeks.incl	the mean number of weeks included in the ALERT period with counts less than threshold
duration.diff	if target.pct specified, the mean difference between the duration of the ALERT period and the duration of the shortest period needed to capture target.pct using postcastALERT.

Author(s)

Nicholas G Reich and Stephen A Lauer

See Also

createALERT

Examples

## view the performance of ALERT over three levels of minimum case percentage and maximum duration length
data(fluData)
robustALERT(minPercent=c(.8, .85, .9), maxDuration=c(12, 13, 14), data=fluData, k=2, target.pct=0.85)

reichlab/ALERT documentation built on Jan. 8, 2020, 7:26 p.m.