CMA5 | R Documentation |
Constructs a CMA (continuous multiple-interval measures of medication availability/gaps) type 5 object.
CMA5( data = NULL, ID.colname = NA, event.date.colname = NA, event.duration.colname = NA, event.daily.dose.colname = NA, medication.class.colname = NA, medication.groups = NULL, flatten.medication.groups = FALSE, medication.groups.colname = ".MED_GROUP_ID", 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.start.per.medication.group = FALSE, 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, suppress.special.argument.checks = TRUE, arguments.that.should.not.be.defined = c(carryover.within.obs.window = TRUE, carryover.into.obs.window = FALSE), ... )
data |
A |
ID.colname |
A string, the name of the column in |
event.date.colname |
A string, the name of the column in
|
event.duration.colname |
A string, the name of the column in
|
event.daily.dose.colname |
A string, the name of the column in
|
medication.class.colname |
A string, the name of the column in
|
medication.groups |
A vector of characters defining medication
groups or the name of a column in |
flatten.medication.groups |
Logical, if |
medication.groups.colname |
a string (defaults to ".MED_GROUP_ID")
giving the name of the column storing the group name when
|
carry.only.for.same.medication |
Logical, if |
consider.dosage.change |
Logical, if |
followup.window.start |
If a |
followup.window.start.unit |
can be either "days",
"weeks", "months" or "years", and represents the time
units that |
followup.window.start.per.medication.group |
a logical: if there are
medication groups defined and this is |
followup.window.duration |
either a number representing the
duration of the follow-up window in the time units given in
|
followup.window.duration.unit |
can be either "days",
"weeks", "months" or "years", and represents the time
units that |
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
|
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 |
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 |
force.NA.CMA.for.failed.patients |
Logical describing how the
patients for which the CMA estimation fails are treated: if |
parallel.backend |
Can be "none" (the default) for single-threaded
execution, "multicore" (using |
parallel.threads |
Can be "auto" (for |
suppress.warnings |
Logical, if |
suppress.special.argument.checks |
Logical parameter for internal
use; if |
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 |
CMA5
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 and the last event,
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 start of the last event within the observation window.
The formula is
(number of days of theoretical use) / (first to last event)
Observations:
the carry.only.for.same.medication
parameter controls the
transmission of carry-over across medication changes, producing a "standard"
CMA5
(default value is FALSE), and an "alternative" CMA5b
,
respectively;
the consider.dosage.change
parameter controls if dosage changes
are taken into account, i.e. if set as TRUE and a new medication event has a
different daily dosage recommendation, carry-over is recomputed assuming
medication use according to the new prescribed dosage (default value is FALSE).
An S3
object of class CMA5
(derived from CMA0
)
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).
CMA
the data.frame
containing the actual CMA
estimates for each participant (the ID.colname
column).
Please note that if medication.groups
are defined, then the CMA
and event.info
are named lists, each element containing the CMA and
event.info corresponding to a single medication group (the element's name).
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. doi: 10.1186/1472-6963-12-155.
cma5 <- CMA5(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" );
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