transformdata function

Data transformation

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

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)

Returns

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

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.

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)

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

Author(s)

Jose E. Lozano lozalojo@gmail.com