Creates a PKNCA::PKNCAdata object. — PKNCA_create_data

Creates a PKNCA::PKNCAdata object.

Usage

PKNCA_create_data_object(
  adnca_data,
  mapping = NULL,
  applied_filters = NULL,
  time_duplicate_rows = NULL
)

Arguments

adnca_data: Data frame containing raw or pre-processed ADNCA data.
mapping: Optional named list of column mappings (as produced by the Shiny mapping UI). When provided, the preprocessing pipeline is run internally and NCA exclusion flag columns are derived from mapping$NCAwXRS (plus "DTYPE"). Metabolite names are taken from mapping$Metabolites. Defaults to NULL (no preprocessing, no exclusion columns).
applied_filters: Optional list of filters to apply (see apply_filters()). Only used when mapping is provided. Defaults to NULL.
time_duplicate_rows: Optional integer vector of row indices (in the mapped dataset, before filtering) to mark as "TIME DUPLICATE" in the DTYPE column. When NULL (the default) and time duplicates are detected, an error of class "time_duplicate_error" is raised with the duplicate rows attached. Use this to forward user-resolved selections from the Shiny duplicate resolution modal.

Value

PKNCAdata object with concentration, doses, and units based on ADNCA data.

Details

This function creates a standard PKNCAdata object from raw or pre-processed ADNCA data.

When mapping is provided, the function runs the full preprocessing pipeline internally: column mapping (apply_mapping()), metabolite flagging (create_metabfl()), class/length adjustment (adjust_class_and_length()), duplicate annotation, optional filtering (apply_filters()), and derives NCA exclusion flag columns from mapping$NCAwXRS (plus "DTYPE").

When mapping is NULL (the default), the function expects already pre-processed ADNCA data with the standard column names in place.

The ADNCA data (after preprocessing, if applicable) must contain:

STUDYID: Study identifier.
PCSPEC: Matrix.
ROUTE: Route of administration.
DOSETRT: Drug identifier.
USUBJID: Unique subject identifier.
ATPTREF: (Non-standard column). Can be any column, used for filtering the data for NCA
PARAM: Analyte.
AVAL: Analysis value.
AVALU: AVAL unit.
DOSEA: Dose amount.
DOSEU: Dose unit.
AFRLT: Actual time from first dose.
ARRLT: Actual time from reference dose.
NFRLT: Nominal time from first dose.
ADOSEDUR: Duration of dose.
RRLTU: Time unit.

Then it proceeds to:

Creating pk concentration data using format_pkncaconc_data().
Creating dosing data using format_pkncadose_data().
Creating PKNCAconc object using PKNCA::PKNCAconc() with formula AVAL ~ AFRLT | STUDYID + PCSPEC + DOSETRT + USUBJID / PARAM.
Creating PKNCAdose object using PKNCA::PKNCAdose() with formula DOSEA ~ AFRLT | STUDYID + DOSETRT + USUBJID.
Creating PKNCAdata object using PKNCA::PKNCAdata().
Updating units in PKNCAdata object so each analyte has its own unit.

Examples

adnca_data <- data.frame(
  STUDYID = rep("STUDY001", 6),
  PCSPEC = rep("Plasma", 6),
  ROUTE = rep("IV", 6),
  DOSETRT = rep("DrugA", 6),
  USUBJID = rep("SUBJ001", 6),
  ATPTREF = rep(1, 6),
  PARAM = rep("AnalyteA", 6),
  AVAL = c(0, 5, 10, 7, 3, 1),
  AVALU = rep("ng/mL", 6),
  DOSEA = rep(100, 6),
  DOSEU = rep("mg", 6),
  AFRLT = c(0, 1, 2, 3, 4, 6),
  ARRLT = c(0, 1, 2, 3, 4, 6),
  NFRLT = c(0, 1, 2, 3, 4, 6),
  ADOSEDUR = rep(0.5, 6),
  RRLTU = rep("hour", 6)
)
PKNCA_create_data_object(adnca_data)
#> Formula for concentration:
#>  AVAL ~ AFRLT | STUDYID + PCSPEC + DOSETRT + USUBJID/PARAM
#> <environment: 0x5580edbe94a0>
#> Data are dense PK.
#> With 1 subjects defined in the 'USUBJID' column.
#> Nominal time column is: NFRLT
#> 
#> Data for concentration:
#>   STUDYID PCSPEC ROUTE DOSETRT USUBJID ATPTREF    PARAM AVAL AVALU DOSEA DOSEU
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    0 ng/mL   100    mg
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    5 ng/mL   100    mg
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA   10 ng/mL   100    mg
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    7 ng/mL   100    mg
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    3 ng/mL   100    mg
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    1 ng/mL   100    mg
#>  AFRLT ARRLT NFRLT ADOSEDUR RRLTU CONCDUR nca_exclude     std_route DOSNOA
#>      0     0     0      0.5  hour       0             intravascular      1
#>      1     1     1      0.5  hour       0             intravascular      1
#>      2     2     2      0.5  hour       0             intravascular      1
#>      3     3     3      0.5  hour       0             intravascular      1
#>      4     4     4      0.5  hour       0             intravascular      1
#>      6     6     6      0.5  hour       0             intravascular      1
#>  is.excluded.hl is.included.hl REASON exclude_half.life volume
#>           FALSE          FALSE                    FALSE     NA
#>           FALSE          FALSE                    FALSE     NA
#>           FALSE          FALSE                    FALSE     NA
#>           FALSE          FALSE                    FALSE     NA
#>           FALSE          FALSE                    FALSE     NA
#>           FALSE          FALSE                    FALSE     NA
#>  include_half.life
#>                 NA
#>                 NA
#>                 NA
#>                 NA
#>                 NA
#>                 NA
#> Formula for dosing:
#>  DOSEA ~ AFRLT | STUDYID + DOSETRT + USUBJID
#> Nominal time column is: NFRLT
#> 
#> Data for dosing:
#>   STUDYID PCSPEC ROUTE DOSETRT USUBJID ATPTREF    PARAM AVAL AVALU DOSEA DOSEU
#>  STUDY001 Plasma    IV   DrugA SUBJ001       1 AnalyteA    0 ng/mL   100    mg
#>  AFRLT ARRLT NFRLT ADOSEDUR RRLTU CONCDUR nca_exclude     std_route DOSNOA
#>      0     0     0      0.5  hour       0             intravascular      1
#>  is.excluded.hl is.included.hl REASON exclude_half.life exclude
#>           FALSE          FALSE                    FALSE    <NA>
#> 
#> With 1 rows of interval specifications.
#> With units
#> With imputation: NA
#> No options are set differently than default.