cover_special_periods {AdhereR}

Cover special periods.

Description

Identifies special periods that are in proximity to already covered durations and adds additional events for these durations.

Usage

cover_special_periods(
  events.data,
  special.periods.data,
  ID.colname,
  medication.class.colnames,
  disp.date.colname,
  disp.start.colname,
  episode.start.colname,
  episode.end.colname,
  duration.colname,
  days.before,
  days.after,
  date.format,
  suppress.warnings = FALSE,
  return.data.table = FALSE,
  ...
)

Arguments

events.data

A data.frame or data.table with the event durations.

special.periods.data

a data.frame or or data.table containing the information about special periods (e.g., hospitalizations or other situations where medication use may differ, e.g. during incarcerations or holidays). Must contain the same unique patient ID as dispensing and prescription data, the start and end dates of the special periods with the exact column names DATE.IN and DATE.OUT.

ID.colname

A string, the name of the column in events.data and special.periods.data containing the unique patient ID.

medication.class.colnames

A Vector of strings, the name(s) of the column(s) in the events.data identify medication classes.

disp.date.colname

A string, the name of the column in events.data containing the dispensation start date (in the format given in the date.format parameter).

disp.start.colname, episode.start.colname, episode.end.colname

column names in events.data.

duration.colname

A string, the name of the column in events.data containing the duration of the medication event.

days.before

an integer, the number of days before the start of a special period within which an event duration must end to consider the special period as covered.

days.after

an integer, the number of days after a special period within which an event duration must start to consider the special period as covered.

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).

suppress.warnings

Logical, if TRUE don't show any warnings.

return.data.table

Logical, if TRUE return a data.table object, otherwise a data.frame.

...

other possible parameters.

Details

Special periods may appear as gaps, possibly leading to underestimation of implementation or even assumption of discontinuation and non-persistence. To consider such periods as covered, this function adds additional durations, for example when it is assumed that hospitalized patients are adherent during the hospitalization period. This function should be used after pruning with prune_event_durations.

Value

A data.frame or data.table, the events.data with the additional durations for special periods covered.

Examples

## Not run: 
# select medication class of interest and compute event durations
disp_data <- durcomp.dispensing[ID == 3 & grepl("J01EE01", ATC.CODE)]
presc_data <- durcomp.prescribing[ID == 3 & grepl("J01EE01", ATC.CODE)]

event_durations_list <- compute_event_durations(disp.data = disp_data,
                                                presc.data = presc_data,
                                                special.periods.data = durcomp.hospitalisation,
                                                special.periods.method = "carryover",
                                                ID.colname = "ID",
                                                presc.date.colname = "DATE.PRESC",
                                                disp.date.colname = "DATE.DISP",
                                                date.format = "%Y-%m-%d",
                                                medication.class.colnames = c("ATC.CODE",
                                                                              "UNIT",
                                                                              "FORM"),
                                                total.dose.colname = "TOTAL.DOSE",
                                                presc.daily.dose.colname = "DAILY.DOSE",
                                                presc.duration.colname = "PRESC.DURATION",
                                                visit.colname = "VISIT",
                                                force.init.presc = TRUE,
                                                force.presc.renew = TRUE,
                                                split.on.dosage.change = TRUE,
                                                trt.interruption = "carryover",
                                                suppress.warnings = FALSE,
                                                return.data.table = TRUE,
                                                progress.bar = FALSE)

event_durations <- prune_event_durations(event_durations_list,
                                         include = c("special periods"),
                                         medication.class.colnames = "ATC.CODE",
                                         days.within.out.date.1 = 7,
                                         days.within.out.date.2 = 30,
                                         keep.all = TRUE)

# cover special periods
special_periods <- event_durations_list$special_periods
event_durations_covered <- cover_special_periods(events.data = event_durations,
                                                 special.periods.data = special_periods,
                                                 ID.colname = "ID",
                                                 medication.class.colnames = "ATC.CODE",
                                                 disp.start.colname = "DISP.START",
                                                 duration.colname = "DURATION",
                                                 days.before = 7,
                                                 days.after = 7,
                                                 date.format = "%Y-%m-%d")
       
## End(Not run)