R: CMA constructor for polypharmacy.

CMA_polypharmacy {AdhereR}

R Documentation

CMA constructor for polypharmacy.

Description

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

Usage

CMA_polypharmacy(
  data = data,
  medication.groups = medication.class.colname,
  CMA.to.apply = NA,
  aggregate.first = TRUE,
  aggregation.method = NA,
  aggregation.method.arguments = NA,
  thresholds = NA,
  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 = NA,
  consider.dosage.change = NA,
  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 = "CMA for polypharmacy",
  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

`data`	A `data.frame` containing the events (prescribing or dispensing) used to compute the CMA. Must contain, at a minimum, the patient unique ID, the event date and duration, medication type, and might also contain the daily dosage (the actual column names are defined in the following four parameters).
`medication.groups`	A string with the name of the column containing the medication groups. If multiple medication classes should belong to the same treatment group, they can be differentiated here (important to investigate treatment switches)
`CMA.to.apply`	A string giving the name of the CMA function (1 to 9) that will be computed for each treatment group.
`aggregate.first`	Logical, if `TRUE`, aggregate across treatment groups before summarizing over time during OW.
`aggregation.method`	A string giving the name of the function to aggregate CMA values of medication group, or `NA` to return only raw CMA estimates per medication group. Accepts summary functions such as "mean", "sd", "var", "min", "max", and "median". Custom functions are possible as long as they take a numeric vector as input and return a single numeric value.
`aggregation.method.arguments`	optional, A named list of additional arguments to the function given in `aggregation method`, e.g. `na.rm = TRUE`.
`thresholds`	optional, a number to apply as threshold between aggregation and summarizing.
`ID.colname`	A string, the name of the column in `data` containing the medication type. Defaults to `medication.class.colname`.
`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; valid only for CMAs 5 to 9, in which case it is coupled (i.e., the same value is used for computing the treatment episodes and the CMA on each treatment episode).
`consider.dosage.change`	Logical, if `TRUE`, the carry-over is adjusted to also reflect changes in dosage; valid only for CMAs 5 to 9, in which case it is coupled (i.e., the same value is used for computing the treatment episodes and the CMA on each treatment episode).
`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). Can be defined separately for each patient and treatment group.
`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.
`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.
`suppress.special.argument.checks`	Logical parameter for internal use; if `FALSE` (default) check if the important columns in the `data` have some of the reserved names, if `TRUE` this check is not performed.
`...`	other possible parameters

Value

An S3 object of class CMA_polypharmacy 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).
aggregation.method the aggregation method to combine CMA values from different groups.
computed.CMA the class name of the computed CMA.
medication.groups a data.frame with medication groups and classes
CMA the data.frame containing the actual CMA estimates for each participant (the ID.colname column) and sometimes treatment group, with columns:
- ID.colname the patient ID as given by the ID.colname parameter.
- medication.groups only when no aggregation method is used (aggregation.method = NA); the treatment group as given by the medication.groups parameter.
- CMA the treatment episode's estimated CMA.

Examples

## Not run: 
CMA_PP <- CMA_polypharmacy(data = med.events.pp,
medication.groups = med.groups,
CMA.to.apply = "CMA7",
aggregate.first = TRUE, # aggregate before summarizing
aggregation.method = "mean", # compute mean of CMAs
aggregation.method.arguments = list(na.rm = TRUE), # remove NA's during calculation
thresholds = NA, # don't apply threshold
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,
observation.window.start=180,
observation.window.duration=365,
carry.only.for.same.medication = TRUE);
## End(Not run)

[Package AdhereR version 0.8.1 Index]