AlgoParam: List of datasets containing the Farrington Flexible and GLRNB...

In EpiSignalDetection: Signal Detection Analysis

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

1. 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

2. 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

EpiSignalDetection documentation built on Dec. 11, 2021, 9:27 a.m.