For a given event (prescribing or dispensing) database, compute the gap days and event intervals in various scenarious.
compute.event.int.gaps(
data,
ID.colname = NA,
event.date.colname = NA,
event.duration.colname = NA,
event.daily.dose.colname = NA,
medication.class.colname = NA,
event.interval.colname = "event.interval",
gap.days.colname = "gap.days",
carryover.within.obs.window = FALSE,
carryover.into.obs.window = FALSE,
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",
keep.window.start.end.dates = FALSE,
remove.events.outside.followup.window = TRUE,
keep.event.interval.for.all.events = FALSE,
parallel.backend = c("none", "multicore", "snow", "snow(SOCK)", "snow(MPI)",
"snow(NWS)")[1],
parallel.threads = "auto",
suppress.warnings = FALSE,
return.data.table = FALSE,
...
)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.
A string, the name of the column in data
containing the unique patient ID; must be present.
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.
A string, the name of the column in
data containing the event duration (in days); must be present.
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 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.
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.
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 medication 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); 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.
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.
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).
Logical, should the computed start and end dates of the windows be kept?
Logical, should the events that fall outside the follo-wup window be removed from the results?
Logical, should the computed
event intervals be kept for all events, or NA'ed for those outside the
OW?
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).
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).
Logical, if TRUE don't show any
warnings.
Logical, if TRUE return a
data.table object, otherwise a data.frame.
extra arguments.
A data.frame or data.table extending the
event.info parameter with:
event.interval Or any other name given in
event.interval.colname, containing the number of days between the
start of the current event and the start of the next one.
gap.days Or any other name given in gap.days.colname,
containing the number of days when medication was not available for the
current event (i.e., the "gap days").
.FU.START.DATE,.FU.END.DATE if kept, the actual start and end
dates of the follow-up window (after adjustments due to the various
parameters).
.OBS.START.DATE,.OBS.END.DATE if kept, the actual start and end
dates of the observation window (after adjustments due to the various
parameters).
.EVENT.STARTS.BEFORE.OBS.WINDOW if kept, TRUE if the
current event starts before the start of the observation window.
.TDIFF1,.TDIFF2 if kept, various auxiliary time differences
(in days).
.EVENT.STARTS.AFTER.OBS.WINDOW if kept, TRUE if the
current event starts after the end of the observation window.
.CARRY.OVER.FROM.BEFORE if kept, the carry-over (if any) from
the previous events.
.EVENT.WITHIN.FU.WINDOW if kept, TRUE if the current
event is within the follow-up window.
This should in general not be called directly by the user, but is provided as a basis for the extension to new CMAs.