transformdata: Data transformation

In mem: The Moving Epidemic Method

Data transformation

Description

Function transformdata transforms data from year,week,rate to week,rate1,...,rateN suitable to use with mem.

Usage

transformdata(
  i.data,
  i.range.x = NA,
  i.name = "rates",
  i.max.na.per = 100,
  i.function = NULL
)

Arguments

i.data	Data frame of input data.
i.range.x	First and last surveillance week.
i.name	Name of the column to transform.
i.max.na.per	maximum percentage of na's in a season allowable, otherwise, the season is removed
i.function	function used to aggregate data when duplicate values are found for the same season and week, defaults to NULL (no aggregate function)

Details

Transform data from format year, week, rate to a format suitable to be used with mem, that is, one column with each season in the dataset and the week names as rownames of the data.frame.

Value

transformdata returns a data.frame where each column has a different season and rownames are the name of the epidemiological week.

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(flucylraw)
# Transform data
newdata <- transformdata(flucylraw, i.range.x = c(40, 20))$data
epi <- memmodel(newdata)
print(epi)
summary(epi)
plot(epi)

mem documentation built on July 9, 2023, 6:34 p.m.