Skip to contents

Summary Concentration Table (pkct01)

Source: R/t_pkct01.R
t_pkct01.Rd

Summarizes PK concentration data by treatment/dose group and nominal timepoint. Returns one data frame per analyte/specimen combination containing descriptive statistics across subjects at each scheduled timepoint.

Usage

t_pkct01(
  data,
  list_vars = c("PARAM", "PCSPEC"),
  strat_var = c("TRT01A", "ATPTREF", "NFRLT"),
  value_var = "AVAL",
  blq_var = "AVALC",
  time_var = "NFRLT",
  time_filter = NULL,
  col_group_var = NULL,
  stats = NULL
)

t_pkct01_dose(data, strat_var = c("DOSEA", "ATPTREF", "NFRLT"), ...)

t_pkct01_tad(data, strat_var = c("TRT01A", "ATPTREF", "NRRLT"), ...)

t_pkct01_dose_tad(data, strat_var = c("DOSEA", "ATPTREF", "NRRLT"), ...)

Arguments

data

A CDISC ADNCA data frame (from export_cdisc()$adnca).

list_vars

Character vector of columns used to split the output into separate tables. Default: c("PARAM", "PCSPEC").

strat_var

One or more columns whose combination defines the table rows (stratification). Default: c("TRT01A", "ATPTREF", "NFRLT") – treatment arm, visit reference, and nominal timepoint. Add or remove columns to change how the rows are grouped. Any variable that is also a list_vars (table-split) column is dropped from the rows, since it is constant within each split.

value_var

Column containing the numeric analysis value. Default: "AVAL".

blq_var

Column containing the character analysis value used to detect BLQ records. Default: "AVALC". Records where this column equals "BLQ" are counted separately and excluded from numeric summaries. When blq_var is absent (as in export_cdisc()$adnca, which does not include AVALC), BLQ is detected via value_var == 0, consistent with the package convention for post-imputation BLQ encoding.

time_var

Column that the time_filter applies to (the nominal timepoint column). Default: "NFRLT". Row grouping is controlled entirely by strat_var; this argument only names the column that time_filter subsets.

time_filter

Optional vector of time_var values to keep. NULL (default) keeps every timepoint.

col_group_var

Optional subject-level column (e.g. "SEX", "RACE") whose values become side-by-side comparison column groups: the full statistic block is repeated once per level, nested under a group header. NULL (default) produces the standard flat table. Must differ from strat_var and the list_vars.

stats

Optional character vector of statistics to display, chosen from c("n", "n_blq", "Mean", "SD", "CV_pct", "Median", "GeoMean", "GeoCV_pct", "Min", "Max"). NULL (default) shows all of them.

...

Additional arguments forwarded to t_pkct01().

Value

A named list of data frames, one per unique combination of list_vars. Each data frame has one column per strat_var followed by the statistics: n, n_blq, Mean, SD, CV_pct, Median, GeoMean, GeoCV_pct, Min, Max. When col_group_var is set, the statistic columns are prefixed per group level and a col_groups attribute drives the rendered two-level header.

Details

BLQ values are excluded from all numeric statistics and counted in n_blq. When blq_var is present, BLQ is identified as df[[blq_var]] == "BLQ". When blq_var is absent, value_var == 0 is used as the fallback BLQ indicator. GeoMean is computed on positive value_var values only.

Functions

  • t_pkct01_dose(): Stratify by dose instead of treatment arm (first dose).

  • t_pkct01_tad(): Summarize using time after dose (TAD) nominal time.

  • t_pkct01_dose_tad(): Stratify by dose using TAD nominal time.

Examples

if (FALSE) { # \dontrun{
adnca <- export_cdisc(res_nca)$adnca
tables <- t_pkct01(adnca)
tables[[1]]
} # }