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Last data update: 2014.03.03

R: Thresholds for influenza intensity

memintensity

R Documentation

Thresholds for influenza intensity

Description

Function memintensity is used to calculate the thresholds for influenza activity using historical records (surveillance rates).
This method is based on the Moving Epidemics Method (MEM) used to monitor influenza activity in a weekly surveillance system.

Usage

memintensity(i.data, i.levels = c(0.40,0.90,0.975), i.n.max = -1, i.seasons = 10)

Arguments

`i.data`	Data frame of input data.
`i.levels`	Levels of the intensity thresholds.
`i.n.max`	Number of epidemic values used to calculate the intensity thresholds.
`i.seasons`	Maximum number of seasons to use.

Details

Input data is a data frame containing rates that represent historical influenza surveillance data. It can start and end at any given week (tipically at week 40th), and rates can be expressed as per 100,000 inhabitants (or per consultations, if population is not available) or any other scale.
MEM is used to locate the epidemic for each season. Then confidence intervals are calculated at different levels.
The parameter i.levels, define the three levels of the confidence intervals used to calculate thresholds.
The i.n.max parameter indicates how many epidemic values to use to calculate the thresholds. A value of -1 indicates the program to use an appropiate number of points depending on the number of seasons provided as input.
The i.seasons parameter indicates how many seasons are used for calculating thresholds. A value of -1 indicates the program to use as many as possible. If there are less than this parameter, the program used all seasons avalaible.
Intensity thresholds and Epidemic threshold defines 5 levels of intensity:

	`1`	Baseline level - Below epidemic threshold.
	`2`	Low level - Above epidemic threshold and below low intensity threshold.
	`3`	Medium level - Above low intensity threshold and below medium intensity threshold.
	`4`	High level - Above medium intensity threshold and below high intensity threshold.
	`5`	Very high level - Above high intensity threshold.

Value

memintensity returns a list with three objects, two of them are the parameters used (param.levels and param.seasons) and the third one (intensity.thresholds) is a matrix 1x4 with the epidemic and intensity thresholds.

	`1`	Epidemic threshold.
	`2`	Low intensity threshold.
	`3`	Medium intensity threshold.
	`4`	High intensity threshold.

Author(s)

Jose E. Lozano Alonso <lozalojo@jcyl.es>.

References

Vega T., Lozano J.E. (2004) Modelling influenza epidemic - can we detect the beginning and predict the intensity and duration? International Congress Series 1263 (2004) 281-283.
Vega T., Lozano J.E. (2012) Influenza surveillance in Europe: establishing epidemic thresholds by the Moving Epidemic Method. Influenza and Other Respiratory Viruses, DOI:10.1111/j.1750-2659.2012.00422.x.

Examples

## Castilla y Leon Influenza Rates data 
data(flucyl)
## Finds the timing of the first season: 2001/2002
intensity<-memintensity(flucyl)
intensity