createALERT: Producing the ALERT thresholds table

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

Description

The createALERT function calculates the ALERT thresholds table given data and other parameters.

Usage

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

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.
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	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 (optional)
caseColumn	the name of the column with the case counts in it. Defaults to 'Cases'
lastDate	a string in unambigous date format. All cases after this date will be removed prior to running the createALERT algorithm

Value

By utilizing the applyALERT function, createALERT uses prior hospital data to prospectively determine the start and end to a period of elevated influenza incidence in a community.

createALERT()$details creates a list of matrices. Each matrix contains raw statistics for the performance of a threshold for each flu season in data (these statistics can be found in applyALERT).

createALERT()$out produces a matrix summarizing the performance of different ALERT thresholds. The columns for this matrix are as follows:

threshold	the minimum threshold number of cases needed to begin the ALERT period
median.dur	the median ALERT period duration in weeks
median.pct.cases.captured	across all seasons, the median percentage of all influenza cases contained within the ALERT period
min.pct.cases.captured	the minimum percentage of annual cases captured during the ALERT period in any season
max.pct.cases.captured	the maximum percentage of annual cases captured during the ALERT period in any season
pct.peaks.captured	the percentage of seasons in which the ALERT period contained the peak week
pct.ext.peaks.captured	the percentage of seasons in which the ALERT period contained the peak week +/- k weeks
median.low.weeks.incl	the median number of weeks included in the ALERT period with counts less than threshold
median.duration.diff	if target.pct specified, the median difference between the duration of the ALERT period in a season and the duration of the shortest period needed to capture target.pct of cases for that season

Author(s)

Nicholas G Reich and Stephen A Lauer

See Also

evalALERT cross-validates ALERT data over a rule

robustALERT cross-validates ALERT data over a series of rules

Examples

## Find the ALERT thresholds table for fluData over all thresholds
data(fluData)
x <- createALERT(data=fluData, allThresholds=TRUE, k=2, target.pct=0.85)
x$out

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