mem (version 2.18)

memsurveillance.animated: Creates the animated graph of the surveillance of the current season

Description

Function memsurveillance.animated creates an animated surveillance graph for the current season.

Usage

memsurveillance.animated(
  i.current,
  i.epidemic.thresholds = NA,
  i.intensity.thresholds = NA,
  i.output = ".",
  i.animated.graph.file = T,
  i.animated.graph.file.name = "animated",
  i.fps = 2,
  i.loop = 0,
  i.remove = T,
  ...
)

Value

memsurveillance.animated writes a gif graph of the surveillance of this season.

Arguments

i.current

Current season weekly rates.

i.epidemic.thresholds

Pre and post epidemic threholds.

i.intensity.thresholds

Intensity thresholds.

i.output

Directory where graph is saved.

i.animated.graph.file

If a animated gif should be produced, or just the intermediate graphics

i.animated.graph.file.name

Name of the animated graph.

i.fps

Number of frames per second of the animated gif.

i.loop

Number of loops for the animated dif, 0 for Infinite.

i.remove

Remove partial graphs.

...

Additional parameters parsed to memsurveillance.

Author

Jose E. Lozano

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.

See memsurveillance for more details

References

Vega T, Lozano JE, Ortiz de Lejarazu R, Gutierrez Perez M. Modelling influenza epidemic - can we detect the beginning and predict the intensity and duration? Int Congr Ser. 2004 Jun;1263:281-3.

Vega T, Lozano JE, Meerhoff T, Snacken R, Mott J, Ortiz de Lejarazu R, et al. Influenza surveillance in Europe: establishing epidemic thresholds by the moving epidemic method. Influenza Other Respir Viruses. 2013 Jul;7(4):546-58. DOI:10.1111/j.1750-2659.2012.00422.x.

Vega T, Lozano JE, Meerhoff T, Snacken R, Beaute J, Jorgensen P, et al. Influenza surveillance in Europe: comparing intensity levels calculated using the moving epidemic method. Influenza Other Respir Viruses. 2015 Sep;9(5):234-46. DOI:10.1111/irv.12330.

Lozano JE. lozalojo/mem: Second release of the MEM R library. Zenodo [Internet]. [cited 2017 Feb 1]; Available from: https://zenodo.org/record/165983. DOI:10.5281/zenodo.165983

Examples

# \donttest{
# 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(".")
# uncomment to execute
# m1 <- memsurveillance.animated(cur,
#    i.animated.graph.file.name = "Animated",
#    i.epidemic.thresholds = e.thr, i.intensity.thresholds = i.thr, i.pos.epidemic = TRUE,
#    i.animated.graph.file = FALSE
# )
# }