memsurveillance: Creates the surveillance graph of the current season

Description Usage Arguments Details Value Author(s) References Examples

View source: R/memsurveillance.R

Description

Function memsurveillance creates a surveillance graph for the current season.

Usage

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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,
  i.mem.info = 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.

i.mem.info

include information about the package in the graph.

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.

Surveillance consist on:

  1. Draw weekly values along with the pre-epidemic threshold.

  2. When the weekly value rises above the threshold a marker of the start of the epidemic is placed and the intensity thresholds are drawn.

  3. When the weekly value goes down the post-epidemic threshold, the marker of the end of the epidemic is placed and the post-epidemic threshold is added to the graph.

The Surveillance Week allows select the week to use in the surveillance, the values of the surveillance season are shown only up to this week, and the program will ignore values past this week.

The Force epidemic start allows to force the placement of the epidemic start marker at a given week instead of using the first week above the epidemic threshold.

Value

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

Author(s)

Jose E. Lozano lozalojo@gmail.com

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

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# 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
# uncomment to execute
# 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
# )

lozalojo/mem documentation built on Sept. 15, 2020, 1:12 a.m.