compute.event.int.gaps {AdhereR}

Gap Days and Event (prescribing or dispensing) Intervals.

Description

For a given event (prescribing or dispensing) database, compute the gap days and event intervals in various scenarious.

Usage

compute.event.int.gaps(
  data,
  ID.colname = NA,
  event.date.colname = NA,
  event.duration.colname = NA,
  event.daily.dose.colname = NA,
  medication.class.colname = NA,
  event.interval.colname = "event.interval",
  gap.days.colname = "gap.days",
  carryover.within.obs.window = FALSE,
  carryover.into.obs.window = FALSE,
  carry.only.for.same.medication = FALSE,
  consider.dosage.change = FALSE,
  followup.window.start = 0,
  followup.window.start.unit = c("days", "weeks", "months", "years")[1],
  followup.window.duration = 365 * 2,
  followup.window.duration.unit = c("days", "weeks", "months", "years")[1],
  observation.window.start = 0,
  observation.window.start.unit = c("days", "weeks", "months", "years")[1],
  observation.window.duration = 365 * 2,
  observation.window.duration.unit = c("days", "weeks", "months", "years")[1],
  date.format = "%m/%d/%Y",
  keep.window.start.end.dates = FALSE,
  remove.events.outside.followup.window = TRUE,
  keep.event.interval.for.all.events = FALSE,
  parallel.backend = c("none", "multicore", "snow", "snow(SOCK)", "snow(MPI)",
    "snow(NWS)")[1],
  parallel.threads = "auto",
  suppress.warnings = FALSE,
  suppress.special.argument.checks = FALSE,
  return.data.table = FALSE,
  ...
)

Arguments

data

A data.frame containing the events used to compute the CMA. Must contain, at a minimum, the patient unique ID, the event date and duration, and might also contain the daily dosage and medication type (the actual column names are defined in the following four parameters); the CMA constructors call this parameter data.

ID.colname

A string, the name of the column in data containing the unique patient ID; must be present.

event.date.colname

A string, the name of the column in data containing the start date of the event (in the format given in the date.format parameter); must be present.

event.duration.colname

A string, the name of the column in data containing the event duration (in days); must be present.

event.daily.dose.colname

A string, the name of the column in data containing the prescribed daily dose, or NA if not defined.

medication.class.colname

A string, the name of the column in data containing the classes/types/groups of medication, or NA if not defined.

event.interval.colname

A string, the name of a newly-created column storing the number of days between the start of the current event and the start of the next one; the default value "event.interval" should be changed only if there is a naming conflict with a pre-existing "event.interval" column in event.info.

gap.days.colname

A string, the name of a newly-created column storing the number of days when medication was not available (i.e., the "gap days"); the default value "gap.days" should be changed only if there is a naming conflict with a pre-existing "gap.days" column in event.info.

carryover.within.obs.window

Logical, if TRUE consider the carry-over within the observation window, or NA if not defined.

carryover.into.obs.window

Logical, if TRUE consider the carry-over from before the starting date of the observation window, or NA if not defined.

carry.only.for.same.medication

Logical, if TRUE the carry-over applies only across medication of the same type, or NA if not defined.

consider.dosage.change

Logical, if TRUE the carry-over is adjusted to reflect changes in dosage, or NA if not defined.

followup.window.start

If a Date object, it represents the actual start date of the follow-up window; if a string it is the name of the column in data containing the start date of the follow-up window either as the numbers of followup.window.start.unit units after the first event (the column must be of type numeric) or as actual dates (in which case the column must be of type Date); if a number it is the number of time units defined in the followup.window.start.unit parameter after the begin of the participant's first event.

followup.window.start.unit

can be either "days", "weeks", "months" or "years", and represents the time units that followup.window.start refers to (when a number), or NA if not defined.

followup.window.duration

either a number representing the duration of the follow-up window in the time units given in followup.window.duration.unit, or a string giving the column containing these numbers. Should represent a period for which relevant medication events are recorded accurately (e.g. not extend after end of relevant treatment, loss-to-follow-up or change to a health care provider not covered by the database).

followup.window.duration.unit

can be either "days", "weeks", "months" or "years", and represents the time units that followup.window.duration refers to, or NA if not defined.

observation.window.start, observation.window.start.unit, observation.window.duration, observation.window.duration.unit

the definition of the observation window (see the follow-up window parameters above for details).

date.format

A string giving the format of the dates used in the data and the other parameters; see the format parameters of the as.Date function for details (NB, this concerns only the dates given as strings and not as Date objects).

keep.window.start.end.dates

Logical, should the computed start and end dates of the windows be kept?

remove.events.outside.followup.window

Logical, should the events that fall outside the follo-wup window be removed from the results?

keep.event.interval.for.all.events

Logical, should the computed event intervals be kept for all events, or NA'ed for those outside the OW?

parallel.backend

Can be "none" (the default) for single-threaded execution, "multicore" (using mclapply in package parallel) for multicore processing (NB. not currently implemented on MS Windows and automatically falls back on "snow" on this platform), or "snow", "snow(SOCK)" (equivalent to "snow"), "snow(MPI)" or "snow(NWS)" specifying various types of SNOW clusters (can be on the local machine or more complex setups – please see the documentation of package snow for details; the last two require packages Rmpi and nws, respectively, not automatically installed with AdhereR).

parallel.threads

Can be "auto" (for parallel.backend == "multicore", defaults to the number of cores in the system as given by options("cores"), while for parallel.backend == "snow", defaults to 2), a strictly positive integer specifying the number of parallel threads, or a more complex specification of the SNOW cluster nodes for parallel.backend == "snow" (see the documentation of package snow for details).

suppress.warnings

Logical, if TRUE don't show any warnings.

suppress.special.argument.checks

Logical parameter for internal use; if FALSE (default) check if the important columns in the data have some of the reserved names, if TRUE this check is not performed.

return.data.table

Logical, if TRUE return a data.table object, otherwise a data.frame.

...

extra arguments.

Details

This should in general not be called directly by the user, but is provided as a basis for the extension to new CMAs.

Value

A data.frame or data.table extending the event.info parameter with:

• event.interval Or any other name given in event.interval.colname, containing the number of days between the start of the current event and the start of the next one.

• gap.days Or any other name given in gap.days.colname, containing the number of days when medication was not available for the current event (i.e., the "gap days").

• .FU.START.DATE,.FU.END.DATE if kept, the actual start and end dates of the follow-up window (after adjustments due to the various parameters).

• .OBS.START.DATE,.OBS.END.DATE if kept, the actual start and end dates of the observation window (after adjustments due to the various parameters).

• .EVENT.STARTS.BEFORE.OBS.WINDOW if kept, TRUE if the current event starts before the start of the observation window.

• .TDIFF1,.TDIFF2 if kept, various auxiliary time differences (in days).

• .EVENT.STARTS.AFTER.OBS.WINDOW if kept, TRUE if the current event starts after the end of the observation window.

• .CARRY.OVER.FROM.BEFORE if kept, the carry-over (if any) from the previous events.

• .EVENT.WITHIN.FU.WINDOW if kept, TRUE if the current event is within the follow-up window.