memsurveillance: Creates the surveillance graph of the current season

In lozalojo/mem: The Moving Epidemic Method

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,
  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 [e-mail]

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

# 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 July 7, 2023, 10 a.m.