memtrend: Methods for influenza trend calculation

Description Usage Arguments Details Value Author(s) References Examples

View source: R/memtrend.R

Description

Function memtrend is used to calculate the two parameters for defining the current influenza trend.
This method is based on the Moving Epidemics Method (MEM) used to monitor influenza activity in a weekly surveillance system.

Usage

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memtrend(i.flu, i.type = 1, i.level = 0.95, i.type.boot = "norm",
  i.iter.boot = 10000)

Arguments

i.flu

An object of class mem.

i.type

Type of confidence interval to calculate the trend thresholds.

i.level

Level of confidence interval to calculate the trend thresholds.

i.type.boot

Type of bootstrap technique.

i.iter.boot

Number of bootstrap iterations.

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.
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.
There are three different states for trend, to determine the state, the current rate and the difference of the current and last weekly rate are needed:

2 Ascending - When the weekly rate is above the epidemic threshold and the difference of the current and last weekly rate is higher than Delta OR this is the first time the rate is above the epidemic threshold.
3 Descending - When the weekly rate is above the epidemic threshold and the difference of the current and last weekly rate is lower than Eta OR this is the first time the rate is below the epidemic threshold after having been above it.
1 Stable - Otherwise.

Value

memtrend returns a list with two objects, the first one is the parameter used in the calculations (param.seasons) and the second one (trend.thresholds) is a matrix 1x2 with the Ascending (Delta) and Descending parameters (Eta).

1 Delta - Ascending parameter.
2 Eta - Descending parameter.

Author(s)

Jose E. Lozano lozalojo@gmail.com

References

Vega Alonso, Tomas, Jose E Lozano Alonso, Raul Ortiz de Lejarazu, and Marisol Gutierrez Perez. 2004. Modelling Influenza Epidemic: Can We Detect the Beginning and Predict the Intensity and Duration? International Congress Series, Options for the Control of Influenza V. Proceedings of the International Conference on Options for the Control of Influenza V, 1263 (June): 281-83. doi:10.1016/j.ics.2004.02.121.
Vega, Tomas, Jose Eugenio Lozano, Tamara Meerhoff, Rene Snacken, Joshua Mott, Raul Ortiz de Lejarazu, and Baltazar Nunes. 2013. Influenza Surveillance in Europe: Establishing Epidemic Thresholds by the Moving Epidemic Method. Influenza and Other Respiratory Viruses 7 (4): 546-58. doi:10.1111/j.1750-2659.2012.00422.x.
Vega, Tomas, Jose E. Lozano, Tamara Meerhoff, Rene Snacken, Julien Beaute, Pernille Jorgensen, Raul Ortiz de Lejarazu, et al. 2015. Influenza Surveillance in Europe: Comparing Intensity Levels Calculated Using the Moving Epidemic Method. Influenza and Other Respiratory Viruses 9 (5): 234-46. doi:10.1111/irv.12330.

Examples

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# Castilla y Leon Influenza Rates data
data(flucyl)
# mem model
flucyl.mem<-memmodel(flucyl)
# Calculates trend thresholds
trend<-memtrend(flucyl.mem)
trend

mem documentation built on June 23, 2017, 5:02 p.m.

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