AlgoParam {EpiSignalDetection} | R Documentation |
List of datasets containing the Farrington Flexible and GLRNB default parameters by time unit
Description
A list including two datasets containing the parameters used for Farrington Flexible and for GLRNB for each time unit available in the Signal Detection tool
Usage
AlgoParam
Format
A list of 2 dataframes: one with 2 rows and 9 variables and GRLNB with 2 rows and 8 variables
-
Default parameters for FarringtonFlexible algorithm
- timeunit
Time units available in the signal detection tool i.e. week, month
- w
Window's half-size, i.e. number of weeks to include before and after the current week in each year (w=2 for weeks, w=1 for months)
- reweight
Logical specifying whether to reweight past outbreaks or not (TRUE for both weeks and months, past outbreaks are always reweighted)
- trend
Logical specifying whether a trend should be included and kept in case the conditions in the Farrington et. al. paper are met. (TRUE for both weeks and months, a trend is always fit)
- weightsThreshold
Numeric defining the threshold for reweighting past outbreaks using the Anscombe residuals (2.85 for both weeks and months, as advised in the improved method)
- glmWarnings
Logical specifying whether to print warnings from the call to glm (TRUE for both weeks and months)
- pThresholdTrend
Numeric defining the threshold for deciding whether to keep trend in the model (0.05 for both weeks and months)
- limit54_1
Integer, the number of cases defining a threshold for minimum alarm, no alarm is sounded if fewer than 'limit54_1' cases were reported in the past 'limit54_2' weeks/months
- limit54_2
Integer, the number of periods defining a threshold for minimum alarm, no alarm is sounded if fewer than 'limit54_1' cases were reported in the past 'limit54_2' weeks/months
-
Default parameters for GLRNB algorithm
- timeunit
Time units available in the signal detection tool i.e. week, month
- mu0
A vector of in-control values of the mean of the Poisson / negative binomial distribution with the same length as range - NULL for both weeks and months
- theta
Numeric, the pre-specified value for k or lambda is used in a recursive LR scheme - log(1.2) for both weeks and months corresponding to a 20 percent increase in the mean
- alpha
Numeric, the dispersion parameter of the negative binomial distribution. If alpha=NULL the parameter is calculated as part of the in-control estimation - alpha=NULL for both weeks and months
- cARL
Numeric, the threshold in the GLR test, i.e. c_gamma - cARL=0.25 for both weeks and months
- Mtilde
Integer, the number of observations needed before we have a full rank - Mtilde=1 for both weeks and months
- M
Integer defining the number of time instances back in time in the window-limited approach. To always look back until the first observation use M=-1. M=1 for both weeks and months
- Change
Character string specifying the type of the alternative. Currently the two choices are intercept and epi - Change=intercept for both weeks and months
See Also
surveillance::farringtonFlexible
surveillance::glrnb