Add time since previous dose to data, time of previous dose, most recent dose amount, cumulative number of doses, and cumulative dose amount.

For now, doses have to be in data as EVID=1 and/or EVID=4 records. They can be in the format of one row per dose or repeated dosing notation using ADDL and II.

addTAPD(
  data,
  col.time = "TIME",
  col.evid = "EVID",
  col.amt = "AMT",
  col.tpdos = "TPDOS",
  col.tapd = "TAPD",
  col.pdosamt = "PDOSAMT",
  col.doscuma = "DOSCUMA",
  col.doscumn = "DOSCUMN",
  prefix.cols,
  suffix.cols,
  subset.dos,
  subset.is.complete,
  order.evid = c(3, 0, 2, 4, 1),
  by = "ID",
  SDOS = 1,
  as.fun,
  col.ndoses
)

Arguments

data

The data set to add the variables to.

col.time

Name of time column (created by addTAPD()). Default it "TIME".

col.evid

The name of the event ID column. This must exist in data. Default is EVID.

col.amt

col.evid The name of the dose amount column. This must exist in data. Default is AMT.

col.tpdos

Name of the time of previous dose column (created by addTAPD()). Default is "TPDOS". Set to NULL to not create this column.

col.tapd

Name of the time of previous dose column (created by addTAPD()). Default is "TAPD". Set to NULL to not create this column.

col.pdosamt

The name of the column to be created holding the previous dose amount. Set to NULL to not create this column.

col.doscuma

The name of the column to be created holding the cumulative dose amount. Set to NULL to not create this column.

col.doscumn

The name of the column (created by addTAPD) that holds the cumulative number of doses administered to the subject. Set to NULL to not create this column.

prefix.cols

String to be prepended to all generated column names, that is each of col.tpdos, col.tapd, col.ndoses, col.pdosamt, col.doscuma that are not NULL.

suffix.cols

String to be appended to all generated column names, that is each of col.tpdos, col.tapd, col.ndoses, col.pdosamt, col.doscuma that are not NULL.

subset.dos

A string that will be evaluated as a custom expression to identify relevant events. See subset.is.complete as well.

subset.is.complete

Only used in combination with non-missing subset.dos. By default, subset.dos is used in addition to the impact of col.evid (must be 1 or 4) and col.amt (greater than zero). If subset.is.complete=TRUE, subset.dos is used alone, and col.evid and col.amt are completely ignored. This is typically useful if the events are not doses but other events that are not expressed as a typical dose combination of EVID and AMT columns.

order.evid

Order of events. This will only matter if there are simultaneous events of different event types within subjects. Typically if using nominal time, it may be important to specify whether samples at dosing times are pre-dose samples. The default is c(3,0,4,1,2) - i.e. samples and simulations are pre-dose. See details.

by

Columns to do calculations within. Default is ID.

SDOS

Scaling value for columns related to dose amount, relative to AMT values. col.pdosamt and col.doscuma are affected and will be derived as AMT/SDOSE.

as.fun

The default is to return data as a data.frame. Pass a function (say tibble::as_tibble) in as.fun to convert to something else. If data.tables are wanted, use as.fun="data.table". The default can be configured using NMdataConf.

col.ndoses

Deprecated. Use col.doscumn instead.

Value

A data.frame with additional columns

Details

addTAPD does not require the data to be ordered, and it will not order it. This means you can run addTAPD before ordering data (which may be one of the final steps) in data set preparation. The argument called order.evid is important because of this. If a dosing event and a sample occur at the same time, when which dose was the previous for that sample? Default is to assume the sample is a pre-dose sample, and hence output will be calculated in relation to the dose before. If no dose event is found before, NA's will be assigned.

See also

Other DataCreate: NMorderColumns(), NMstamp(), NMwriteData(), findCovs(), findVars(), flagsAssign(), flagsCount(), mergeCheck(), tmpcol()