Create a PKNCAconc object

Usage

PKNCAconc(data, ...)

# Default S3 method
PKNCAconc(data, ...)

# S3 method for class 'tbl_df'
PKNCAconc(data, ...)

# S3 method for class 'data.frame'
PKNCAconc(
  data,
  formula,
  subject,
  time.nominal,
  exclude = NULL,
  duration,
  volume,
  exclude_half.life,
  include_half.life,
  lloq,
  sparse = FALSE,
  ...,
  concu = NULL,
  amountu = NULL,
  timeu = NULL,
  concu_pref = NULL,
  amountu_pref = NULL,
  timeu_pref = NULL
)

Arguments

data: A data frame with concentration (or amount for urine/feces), time, and the groups defined in formula.
...: Ignored.
formula: The formula defining the concentration~time|groups or amount~time|groups for urine/feces (In the remainder of the documentation, "concentration" will be used to describe concentration or amount.) One special aspect of the groups part of the formula is that the last group to the left of any / is assumed to be the subject unless the subject argument is given. The time may be numeric, or it may be a date-time (POSIXct) or a date (Date); see the "Date-time input" section.
subject: The column indicating the subject number. If not provided, this defaults to the last grouping variable to the left of a / (for example, Subject with concentration~time|Study+Subject/Analyte), or the last grouping variable when there is no / (for example, Subject with concentration~time|Study+Subject). When there are no grouping variables (single-subject data), no subject column is set.
time.nominal: (optional) The name of the nominal time column (if the main time variable is actual time. The time.nominal is not used during calculations; it is available to assist with data summary and checking.
exclude: (optional) The name of a column with concentrations to exclude from calculations and summarization. If given, the column should have values of NA or "" for concentrations to include and non-empty text for concentrations to exclude.
duration: (optional) The duration of collection as is typically used for concentration measurements in urine or feces. The time of a measurement is the start of the collection, and only the time is used when selecting data for a calculation interval; the duration is not considered. A collection starting within an interval and ending after the interval end contributes its full amount to that interval, so for the simplest interpretation of results, align collection start and end times with interval boundaries. A duration column is added to the data only when this is given; requesting an excretion rate parameter (ermax, ertmax, ertlst) without it is an error. A numeric duration is in the time unit of the analysis; a difftime duration is converted to that unit in PKNCAdata().
volume: (optional) The volume (or mass) of collection as is typically used for urine or feces measurements. A volume column is added to the data only when this is given; requesting a parameter that needs it (ae, fe, volpk, and similar) without it is an error.
exclude_half.life, include_half.life: Manual half-life point selection, given as a logical value per concentration measurement (or, in PKNCAconc(), the name of such a column in the data). exclude_half.life drops the flagged points; automatic curve-stripping point selection is still performed on the remaining (non-excluded) points and is not bypassed. include_half.life names the exact points to use, bypassing automatic curve-stripping point selection. Each value is TRUE, FALSE, or NA (undefined); the column/vector is treated as "in use" for an interval unless it is entirely NA (so an all-FALSE column still counts as in use), so leave it NA (rather than FALSE) where the mechanism should not apply. The column must be logical and must exist in the data; anything else is an error. Only one of exclude_half.life and include_half.life may be in use for a given interval. See the "Half-Life Calculation" vignette for more details on the use of these arguments.
lloq: (optional) The lower limit of quantification used by the Tobit half-life method (hl_method = "tobit"). Either the name of a column in data giving the per-observation LLOQ or a numeric scalar applied to all observations. When provided, it is passed through to pk.calc.half.life(). See the "Half-Life Calculation with Tobit Regression" vignette for more details.
sparse: Are the concentration-time data sparse PK (commonly used in small nonclinical species or with terminal or difficult sampling) or dense PK (commonly used in clinical studies or larger nonclinical species)?
concu, amountu, timeu: Either unit values (e.g. "ng/mL") or column names within the data where units are provided. For a date-time (POSIXct or Date) time column, timeu must be a unit value, and timeu_pref takes precedence over it (see the "Date-time input" section).
concu_pref, amountu_pref, timeu_pref: Preferred units for reporting (not column names). For a date-time time column, the times are converted directly to timeu_pref, which then is also timeu.

Value

A PKNCAconc object that can be used for automated NCA.

Date-time input

The concentration time (and the dose time in PKNCAdose()) may be a date-time (POSIXct) or a date (Date; a date is taken as 08:00 on that date, a typical time of a first PK sample, with a warning). Date-times have no numeric unit, so they are converted directly to the time unit used for calculations and reports: timeu_pref when given (it takes precedence over timeu, and timeu is set to it), otherwise timeu, otherwise hours (without units). The unit must be a single time unit value (like "hr" or "day"), not a column name. A numeric duration (here or in PKNCAdose()) is in that unit, and a difftime duration is converted to it exactly.

The times remain date-times in the PKNCAconc, PKNCAdose, and PKNCAdata objects. pk.nca() converts them to numeric time relative to the first dose (or first concentration) in each group; see the "Date-time input" section of PKNCAdata(). The nominal time (time.nominal) is not converted and usually stays numeric.

Create a PKNCAconc object

Usage

Arguments

Value

Date-time input

See also