Description Usage Arguments Value Author(s) See Also Examples
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
.
1 2 3 |
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' |
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 |
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 +/- |
low.weeks.incl |
the mean number of weeks included in the ALERT period with counts less than |
duration.diff |
if |
Nicholas G Reich and Stephen A Lauer
1 2 3 |
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