mem (version 2.5)

memsurveillance: Creates the surveillance graph of the current season

Description

Function memsurveillance creates a surveillance graph for the current season.

Usage

memsurveillance(i.current, i.epidemic.thresholds = NA,
  i.intensity.thresholds = NA, i.mean.length = 10, i.force.length = F,
  i.output = ".", i.graph.title = "", i.graph.subtitle = "",
  i.graph.file = T, i.graph.file.name = "", i.week.report = NA,
  i.equal = F, i.pos.epidemic = F, i.no.epidemic = F,
  i.no.intensity = F, i.epidemic.start = NA, i.range.x = c(40, 20),
  i.range.x.53 = F, i.range.y = NA, i.no.labels = F,
  i.start.end.marks = T)

Arguments

i.current

Current season weekly rates.

i.epidemic.thresholds

Pre and post epidemic threholds.

i.intensity.thresholds

Intensity thresholds.

i.mean.length

Mean length of epidemic.

i.force.length

If you want to force the epidemic to be exactly as the mean length.

i.output

Directory where graph is saved.

i.graph.title

Title of the graph.

i.graph.subtitle

Subtitle of the graph.

i.graph.file

Graph to a file.

i.graph.file.name

Name of the graph.

i.week.report

Week to use in the report.

i.equal

If post epidemic and preepidemic thresholds must be equal (force post epidemic to be equal to the pre epidemic threshold).

i.pos.epidemic

Print post epidemic threhsold.

i.no.epidemic

Force no start of the epidemic, print only the epidemic threshold.

i.no.intensity

Do not print intensity threholds.

i.epidemic.start

Week to force start of the epidemic.

i.range.x

Range of weeks.

i.range.x.53

Is there a week 53 this season.

i.range.y

Range of graph.

i.no.labels

Do not use labels.

i.start.end.marks

Do not place start and end marks of the epidemic.

Value

memsurveillance writes a tiff graph of the surveillance of this season.

Details

Input data must be the current season and an object of class mem. The output graph contains the weekly rates series along with the epidemic and intensity threshols located at the exact situation where the epidemic started. If there is no epidemic yet, only the epidemic threshold is placed.

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

# Castilla y Leon Influenza Rates data
data(flucyl)
# Data of the last season
cur<-flucyl[8]
# The model
epi<-memmodel(flucyl[1:7])
# Epidemic thresholds
e.thr<-epi$epidemic.thresholds
# Intensity threhsolds
i.thr<-epi$intensity.thresholds
# Set the working directory to whererever you want to store the graph file
setwd(".")
# The graph, default values
m1<-memsurveillance(cur,e.thr,i.thr,i.graph.file=TRUE,
     i.graph.file.name="graph 1")
# No intensity levels
m2<-memsurveillance(cur,e.thr,i.thr,i.graph.file=TRUE,
     i.graph.file.name="graph 2",i.no.intensity=TRUE)
# No start/end tickmarks
m3<-memsurveillance(cur,e.thr,i.thr,i.graph.file=TRUE,
     i.graph.file.name="graph 3",i.start.end.marks=FALSE)
# Post-epidemic threshold
m4<-memsurveillance(cur,e.thr,i.thr,i.graph.file=TRUE,
     i.graph.file.name="graph 4",i.pos.epidemic=TRUE)
# Report for week 2, instead of all data
m5<-memsurveillance(cur,e.thr,i.thr,i.graph.file=TRUE,
     i.graph.file.name="graph 5",i.week.report=2)