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Create a PKNCAdata Object for NCA or Slope Analysis

Source: R/PKNCA.R
PKNCA_update_data_object.Rd

This function updates a previously prepared PKNCAdata object based on user selections for method, analyte, dose, specimen, and parameters.

Usage

PKNCA_update_data_object(
  adnca_data,
  method,
  selected_analytes,
  selected_profile,
  selected_pcspec,
  start_impute = TRUE,
  hl_adj_rules = NULL,
  exclusion_list = NULL,
  keep_interval_cols = NULL,
  min_hl_points = 3,
  parameter_selections = NULL,
  int_parameters = NULL,
  blq_imputation_rule = NULL,
  custom_units_table = NULL
)

Arguments

adnca_data

A reactive PKNCAdata object

method

NCA calculation method selection

selected_analytes

User selected analytes

selected_profile

User selected dose numbers/profiles

selected_pcspec

User selected specimen

start_impute

Logical indicating whether to impute start concentration values. Also forwarded to update_main_intervals() when parameter_selections is provided.

hl_adj_rules

A data frame containing half-life adjustment rules. It must contain group columns and rule specification columns; TYPE: (Inclusion, Exclusion), RANGE: (start-end).

exclusion_list

List of exclusion reasons and row indices to apply to the concentration data. Each item in the list should have:

  • reason: character string with the exclusion reason (e.g., "Vomiting")

  • rows: integer vector of row indices to apply the exclusion to

keep_interval_cols

Optional character vector of additional columns to keep in the intervals data frame and when the NCA is run (pk.nca) also in the results

min_hl_points

Minimum number of points to use for half-life calculation. Must be >= 2. Default is 3 (PKNCA default).

parameter_selections

Optional named list of selected PKNCA parameters by study type (forwarded to update_main_intervals()).

int_parameters

Optional data frame containing partial AUC ranges (forwarded to update_main_intervals()).

blq_imputation_rule

Optional list defining the BLQ imputation rule (forwarded to update_main_intervals()).

custom_units_table

Optional data frame with PPSTRESU overrides. When provided, applied via dplyr::rows_update() on the PKNCAdata units table.

Value

A fully configured PKNCAdata object.

Details

Step 1: Update units in the PKNCAdata object ensuring unique analytes have their unique units

Step 2: Set PKNCAoptions for NCA calculation

Step 3: Format intervals using format_pkncadata_intervals()

Step 4: Apply filtering based on user selections and partial aucs

Step 5: Impute start values if requested

Step 6: Indicate points excluded / selected manually for half-life

Step 7 (optional): Update intervals with parameter selections per study type and partial AUC ranges via update_main_intervals().

Step 8 (optional): Apply custom units table for PPSTRESU overrides.

Note*: The function assumes that the adnca_data object has been created using the PKNCA_create_data_object() function.