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CMA_sliding_window

CMA_sliding_window constructor.

Description

Applies a given CMA to each sliding window and constructs a CMA_sliding_window object.

Usage

CMA_sliding_window(
  CMA.to.apply,
  data,
  ID.colname = NA,
  event.date.colname = NA,
  event.duration.colname = NA,
  event.daily.dose.colname = NA,
  medication.class.colname = NA,
  carry.only.for.same.medication = NA,
  consider.dosage.change = NA,
  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],
  sliding.window.start = 0,
  sliding.window.start.unit = c("days", "weeks", "months", "years")[1],
  sliding.window.duration = 90,
  sliding.window.duration.unit = c("days", "weeks", "months", "years")[1],
  sliding.window.step.duration = 30,
  sliding.window.step.unit = c("days", "weeks", "months", "years")[1],
  sliding.window.no.steps = NA,
  date.format = "%m/%d/%Y",
  summary = "CMA per sliding window",
  event.interval.colname = "event.interval",
  gap.days.colname = "gap.days",
  force.NA.CMA.for.failed.patients = TRUE,
  parallel.backend = c("none", "multicore", "snow", "snow(SOCK)", "snow(MPI)",
    "snow(NWS)")[1],
  parallel.threads = "auto",
  suppress.warnings = FALSE,
  ...
)

Arguments

CMA.to.apply

A string giving the name of the CMA function (1 to 9) that will be computed for each treatment episode.
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).
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 medication type, or NA if not defined.
carry.only.for.same.medication

Logical, if TRUE, the carry-over applies only across medication of the same type.
consider.dosage.change

Logical, if TRUE, the carry-over is adjusted to also reflect changes in dosage.
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; 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

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).
sliding.window.start, sliding.window.start.unit, sliding.window.duration, sliding.window.duration.unit

the definition of the first sliding window (see the follow-up window parameters above for details).
sliding.window.step.duration, sliding.window.step.unit

if not missing (NA), these give the step (or "jump") to the right of the sliding window in time units.
sliding.window.no.steps

a integer specifying the desired number of sliding windows to cover the observation window (if possible); trumps sliding.window.step.duration and sliding.window.step.unit.
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).
summary

Metadata as a string, briefly describing this CMA.
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.
force.NA.CMA.for.failed.patients

Logical describing how the patients for which the CMA estimation fails are treated: if TRUE they are returned with an NA CMA estimate, while for FALSE they are omitted.
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.
...

other possible parameters

Details

CMA_sliding_window first computes a set of fixed-size (possibly partly overlapping) sliding windows, each sliding to the right by a fixed timelag, and then, for each of them, it computes the given "simple" CMA. Thus, as opposed to the "simple" CMAs 1 to 9, it returns a set of CMAs, with possibly more than one element.

It is highly similar to CMA_per_episode which computes a CMA for a set of treatment episodes.

Value

An S3 object of class CMA_sliding_window with the following fields:

  • data The actual event data, as given by the data parameter.

  • ID.colname the name of the column in data containing the unique patient ID, as given by the ID.colname parameter.

  • event.date.colname the name of the column in data containing the start date of the event (in the format given in the date.format parameter), as given by the event.date.colname parameter.

  • event.duration.colname the name of the column in data containing the event duration (in days), as given by the event.duration.colname parameter.

  • event.daily.dose.colname the name of the column in data containing the prescribed daily dose, as given by the event.daily.dose.colname parameter.

  • medication.class.colname the name of the column in data containing the classes/types/groups of medication, as given by the medication.class.colname parameter.

  • carry.only.for.same.medication whether the carry-over applies only across medication of the same type, as given by the carry.only.for.same.medication parameter.

  • consider.dosage.change whether the carry-over is adjusted to reflect changes in dosage, as given by the consider.dosage.change parameter.

  • followup.window.start the beginning of the follow-up window, as given by the followup.window.start parameter.

  • followup.window.start.unit the time unit of the followup.window.start, as given by the followup.window.start.unit parameter.

  • followup.window.duration the duration of the follow-up window, as given by the followup.window.duration parameter.

  • followup.window.duration.unit the time unit of the followup.window.duration, as given by the followup.window.duration.unit parameter.

  • observation.window.start the beginning of the observation window, as given by the observation.window.start parameter.

  • observation.window.start.unit the time unit of the observation.window.start, as given by the observation.window.start.unit parameter.

  • observation.window.duration the duration of the observation window, as given by the observation.window.duration parameter.

  • observation.window.duration.unit the time unit of the observation.window.duration, as given by the observation.window.duration.unit parameter.

  • date.format the format of the dates, as given by the date.format parameter.

  • summary the metadata, as given by the summary parameter.

  • event.info the data.frame containing the event info (irrelevant for most users; see compute.event.int.gaps for details).

  • computed.CMA the class name of the computed CMA.

  • CMA the data.frame containing the actual CMA estimates for each participant (the ID.colname column) and sliding window, with columns:

    • ID.colname the patient ID as given by the ID.colname parameter.

    • window.ID the unique window ID (within patients).

    • window.start the window's start date (as a Date object).

    • window.end the window's end date (as a Date object).

    • CMA the window's estimated CMA.

See Also

CMA_per_episode is very similar, computing a "simple" CMA for each of the treatment episodes. The "simple" CMAs that can be computed comprise CMA1, CMA2, CMA3, CMA4, CMA5, CMA6, CMA7, CMA8, CMA9, as well as user-defined classes derived from CMA0 that have a CMA component giving the estimated CMA per patient as a data.frame.

Examples

## Not run: 
cmaW <- CMA_sliding_window(CMA="CMA1",
                           data=med.events,
                           ID.colname="PATIENT_ID",
                           event.date.colname="DATE",
                           event.duration.colname="DURATION",
                           event.daily.dose.colname="PERDAY",
                           medication.class.colname="CATEGORY",
                           carry.only.for.same.medication=FALSE,
                           consider.dosage.change=FALSE,
                           followup.window.start=0,
                           observation.window.start=0,
                           observation.window.duration=365,
                           sliding.window.start=0,
                           sliding.window.start.unit="days",
                           sliding.window.duration=90,
                           sliding.window.duration.unit="days",
                           sliding.window.step.duration=7,
                           sliding.window.step.unit="days",
                           sliding.window.no.steps=NA,
                           date.format="%m/%d/%Y"
                          );
## End(Not run)
AdhereR

Adherence to Medications

v0.6.1
GPL (>= 2)
Authors
Dan Dediu [aut, cre], Alexandra Dima [aut], Samuel Allemann [aut]
Initial release

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