Constructs a basic CMA (continuous multiple-interval measures of medication availability/gaps) object.
CMA0(
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",
carryover.within.obs.window = NA,
carryover.into.obs.window = 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.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 = "Base CMA object",
suppress.warnings = FALSE,
arguments.that.should.not.be.defined = NULL,
...
)A data.frame containing the medication events
(prescribing or dispensing) 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).
A string, the name of the column in data
containing the unique patient ID, or NA if not defined.
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.
A string, the name of the column in
data containing the event duration (in days), or NA if not
defined.
A string, the name of the column in
data containing the prescribed daily dose, or NA if not defined.
A string, the name of the column in
data containing the classes/types/groups of medication, or NA
if not defined.
A vector of characters defining medication
groups or the name of a column in data that defines such groups.
The names of the vector are the medication group unique names, while
the content defines them as logical expressions. While the names can be any
string of characters except "}", it is recommended to stick to the rules for
defining vector names in R. For example,
c("A"="CATEGORY == 'medA'", "AA"="{A} & PERDAY < 4" defines two
medication groups: A which selects all events of type "medA", and
B which selects all events already defined by "A" but with a daily
dose lower than 4. If NULL, no medication groups are defined. If
medication groups are defined, there is one CMA estimate for each group;
moreover, there is a special group __ALL_OTHERS__ automatically defined
containing all observations not covered by any of the explicitly defined
groups.
Logical, if FALSE (the default)
then the CMA and event.info components of the object are lists
with one medication group per element; otherwise, they are data.frames
with an extra column containing the medication group (its name is given by
medication.groups.colname).
a string (defaults to ".MED_GROUP_ID")
giving the name of the column storing the group name when
flatten.medication.groups is TRUE.
Logical, if TRUE consider
the carry-over within the observation window, or NA if not defined.
Logical, if TRUE consider the
carry-over from before the starting date of the observation window, or
NA if not defined.
Logical, if TRUE the
carry-over applies only across medications of the same type, or NA
if not defined.
Logical, if TRUE the carry-over
is adjusted to reflect changes in dosage, or NA if not defined.
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 or a string
that conforms to the format specified in date.format); 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.
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.
a logical: if there are
medication groups defined and this is TRUE, then the first event
considered for the follow-up window start is relative to each medication group
separately, otherwise (the default) it is relative to the patient.
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).
can be either "days",
"weeks", "months" or "years", and represents the time
units that followup.window.duration refers to, or NA if not
defined.
the definition of the observation window (see the follow-up window parameters above for details).
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).
Metadata as a string, briefly describing this CMA.
Logical, if TRUE don't show any
warnings.
a list of argument names and pre-defined valuesfor which a warning should be thrown if passed to the function.
other possible parameters
An S3 object of class CMA0 with the following fields:
data The actual event (prescribing or dispensing) 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.
carryover.within.obs.window whether to consider the carry-over
within the observation window, as given by the
carryover.within.obs.window parameter.
carryover.into.obs.window whether to consider the carry-over
from before the starting date of the observation window, as given by the
carryover.into.obs.window 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.
In most cases this should not be done directly by the user, but it is used internally by the other CMAs.
# NOT RUN {
cma0 <- CMA0(data=med.events,
ID.colname="PATIENT_ID",
event.date.colname="DATE",
event.duration.colname="DURATION",
event.daily.dose.colname="PERDAY",
medication.class.colname="CATEGORY",
followup.window.start=0,
followup.window.start.unit="days",
followup.window.duration=2*365,
followup.window.duration.unit="days",
observation.window.start=30,
observation.window.start.unit="days",
observation.window.duration=365,
observation.window.duration.unit="days",
date.format="%m/%d/%Y",
summary="Base CMA");
# }
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