CMA6: CMA6 constructor.

Description Usage Arguments Details Value See Also Examples

Description

Constructs a CMA (continuous multiple-interval measures of medication availability/gaps) type 6 object.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
CMA6(data = NULL, 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 = 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", summary = NA,
  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.that.should.not.be.defined = c(carryover.within.obs.window =
  TRUE, carryover.into.obs.window = 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).

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).

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.

arguments.that.should.not.be.defined

a list of argument names and pre-defined valuesfor which a warning should be thrown if passed to the function.

...

other possible parameters

Details

CMA6 assumes that, within the observation window, the medication is used as prescribed and new medication is "banked" until needed (oversupply from previous events is used first, followed new medication supply). It computes days of theoretical use by extracting the total number of gap days from the total time interval between the first event and the end of the observation window, accounting for carry over for all medication events within the observation window. Thus, it accounts for timing within the observation window, and excludes the remaining supply at the end of the observation window.

The formula is

(number of days of theoretical use) / (first event to end of observation window)

Observations:

Value

An S3 object of class CMA6 (derived from CMA0) with the following fields:

See Also

CMAs 1 to 8 are defined in:

Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C. (2012). Comparison of pharmacy-based measures of medication adherence. BMC Health Services Research, 12, 155. http://doi.org/10.1186/1472-6963-12-155.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
cma6 <- CMA6(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=30,
             observation.window.start=30,
             observation.window.duration=365,
             date.format="%m/%d/%Y"
            );

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