compute.treatment.episodes: Compute Treatment Episodes.

Description Usage Arguments Details Value

Description

For a given event (prescribing or dispensing) database, compute the treatment episodes for each patient in various scenarious.

Usage

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compute.treatment.episodes(data, ID.colname = NA,
  event.date.colname = NA, event.duration.colname = NA,
  event.daily.dose.colname = NA, medication.class.colname = NA,
  carryover.within.obs.window = TRUE,
  carry.only.for.same.medication = TRUE, consider.dosage.change = TRUE,
  medication.change.means.new.treatment.episode = TRUE,
  dosage.change.means.new.treatment.episode = FALSE,
  maximum.permissible.gap = 90,
  maximum.permissible.gap.unit = c("days", "weeks", "months", "years",
  "percent")[1], 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], event.interval.colname = "event.interval",
  gap.days.colname = "gap.days", date.format = "%m/%d/%Y",
  parallel.backend = c("none", "multicore", "snow", "snow(SOCK)",
  "snow(MPI)", "snow(NWS)")[1], parallel.threads = "auto",
  suppress.warnings = 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, or NA if not defined.

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), or NA if not defined.

event.duration.colname

A string, the name of the column in data containing the event duration (in days), or NA if not defined.

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.

carryover.within.obs.window

Logical, if TRUE consider the carry-over within 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.

medication.change.means.new.treatment.episode

Logical, should a change in medication automatically start a new treatment episode?

dosage.change.means.new.treatment.episode

Logical, should a change in dosage automatically start a new treatment episode?

maximum.permissible.gap

The number of units given by maximum.permissible.gap.unit representing the maximum duration of permissible gaps between treatment episodes (can also be a percent, see maximum.permissible.gap.unit for details).

maximum.permissible.gap.unit

can be either "days", "weeks", "months", "years" or "percent", and represents the time units that maximum.permissible.gap refers to; if percent, then maximum.permissible.gap is interpreted as a percent (can be greater than 100%) of the duration of the current prescription.

followup.window.start

If a Date object it is 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; 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; or NA if not defined.

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

a number representing the duration of the follow-up window in the time units given in followup.window.duration.unit, or NA if not defined.

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.

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.

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).

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.

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.

For the last treatment episode, the gap is considered only when longer than the maximum permissible gap. Please note the following:

Value

A data.frame or data.table with the following columns (or NULL if no treatment episodes could be computed):


AdhereR documentation built on May 2, 2019, 12:40 p.m.