SetOpts: Set all the options for MoMo.
In EuroMOMOnetwork/MOMO: MOMOpack for R

View source: R/aa_MOMOmaster_set_and_run.R

It is usual to run RunMoMo after these options have been set.

SetOpts(
  DoA = as.Date("2015-8-10"),
  DoPR = as.Date("2008-1-1"),
  WStart = 1,
  WEnd = 52,
  country = "Greece",
  source = "UoP",
  MFILE = "greece_m.dta",
  HFILE = "holidayfilegreece.dta",
  INPUTDIR = "./input",
  MDATA = NULL,
  HDATA = NULL,
  WDIR = "./output",
  back = 3,
  WWW = 290,
  Ysum = 2009,
  Wsum = 34,
  USEglm2 = TRUE,
  useAUTOMN = TRUE,
  datesISO = FALSE,
  plotGraphs = TRUE,
  removeDataAfterDoA = TRUE,
  delayVersion = "original",
  delayFunction = NULL,
  delayVariance = FALSE,
  MOMOgroups = list(`0to4` = "age >= 0 & age <=4", `5to14` = "age >= 5 & age <=14",
    `15to64` = "age >= 15 & age <=64", `65P` = "age >= 65 | is.na(age)", Total =
    "age >= 0 | is.na(age)"),
  MOMOmodels = c(`0to4` = "LINE", `5to14` = "LINE", `15to64` = "LINE_SIN", `65P` =
    "LINE_SIN", Total = "LINE_SIN"),
  Ydrop = 9999,
  Wdrop = 99,
  verbose = TRUE
)

`DoA`	Date of aggregation (see specifications, the only information to change weekly). Provided in ISO format, i.e. YYYY-MM-DD.
`DoPR`	Date of start of a regular MOMO registration (see specifications). Provided in ISO format, i.e. YYYY-MM-DD.
`WStart`	Week of cumulative excess start. e.g. "influenza season" as define by EISS will be defined as WStart = 40, WEnd= 20. e.g. summer could be defined as WStart = 26, WEnd= 40
`WEnd`	Week of cumulative excess end e.g. "influenza season" as define by EISS will be defined as WStart = 40, WEnd= 20.
`country`	Country name
`source`	Source of data
`MFILE`	Name of your mortality file, either stata format (.dta) or text file (.txt) [you can use MDATA instead]
`HFILE`	Name of file containing bank Holidays (see specifications), either stata format (.dta) or text file (.txt) [you can use HDATA instead]
`INPUTDIR`	Input directory (where MFILE and HFILE can be found)
`MDATA`	A data.frame containing the data that would have been contained inside MFILE. MDATA takes priority over MFILE if both are specified.
`HDATA`	A data.frame containing the data that would have been contained inside HFILE. HDATA takes priority over HFILE if both are specified.
`WDIR`	Output directory (all output will go here)
`back`	The number of weeks to remove for modeling delay = the part of the series that require delay correction (see specifications).
`WWW`	Length of retrospective historical study period in weeks
`Ysum`	START OF CUSUM CHART: Week for CUSUM to be set to 0
`Wsum`	START OF CUSUM CHART: Week for CUSUM to be set to 0
`USEglm2`	Use glm2() in order to improve convergence properties
`useAUTOMN`	Keep using the column name "Automn" (instead of "Autumn") as in Stata MOMOpack
`datesISO`	When saving dates in text files, use ISO format (standard in R) instead of the Stata "%d" format
`plotGraphs`	Setting this to FALSE suppressess the plotting of the various graphs (and saves time)
`removeDataAfterDoA`	Set this to FALSE to include people who were registered/died after DoA
`delayVersion`	Using the "original" delay code or the "2017-12" delay code
`delayFunction`	This can be used instead of delayVersion. It lets you use a custom delay correction function.
`delayVariance`	If this is true, it means that the prediction variance (from delay correction) is included in the z-scores+confidence interval
`MOMOgroups`	Definition of the groups to be analyzed
`MOMOmodels`	Names in the following vector should correspond to the MOMOgroups and the corresponding values (model to use for each group) should be one of "LINE", "SPLINE", "LINE_SIN", "SPLINE_SIN"
`Ydrop`	Year after which data are not included in the baseline estimation
`Wdrop`	Week of Ydrop after which data are not included in the baseline estimation
`verbose`	Printing out information