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 is typically assumed to be the subject; see the documentation for the subject argument for exceptions to this assumption.
subject: The column indicating the subject number. If not provided, this defaults to the beginning of the inner groups: For example with concentration~time|Study+Subject/Analyte, the inner groups start with the first grouping variable before a /, Subject. If there is only one grouping variable, it is assumed to be the subject (e.g. concentration~time|Subject), and if there are multiple grouping variables without a /, subject is assumed to be the last one. For single-subject data, it is assigned as NULL.
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.
volume: (optional) The volume (or mass) of collection as is typically used for urine or feces measurements.
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. 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.
concu_pref, amountu_pref, timeu_pref: Preferred units for reporting (not column names)

Value

A PKNCAconc object that can be used for automated NCA.

Create a PKNCAconc object

Usage

Arguments

Value

See also