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Mean Urine Amount and Percent Recovered Table (pkpt08)

Source: R/t_pkpt.R
t_pkpt08_uri.Rd

Filters ADPP to urine specimen records and summarizes cumulative amount excreted (Ae) and percentage of dose recovered (Fe%) with descriptive statistics in columns. Per the TLG catalog specification for pkpt08, the summary includes n, Mean, SD, CV%, Median, Min, Max – without geometric mean or geometric CV% (those are omitted because urine recovery parameters are not log-normally distributed by convention).

Usage

t_pkpt08_uri(
  data,
  urine_specs = c("URINE"),
  list_vars = c("PPCAT"),
  strat_var = c("TRT01A", "PARAM"),
  value_var = "AVAL",
  param_filter = NULL,
  col_group_var = NULL,
  stats = NULL
)

Arguments

data

A CDISC ADPP data frame. Urine records are identified by PPSPEC %in% urine_specs.

urine_specs

Character vector of specimen types considered urine, matched case-insensitively. Default: c("URINE").

list_vars

Character vector of columns used to split output into separate tables. Default: c("PPCAT"). AVISIT is a conditional ADPP column that is typically absent from export_cdisc()$adpp; it is silently skipped when not present so there is no need to remove it manually, but adding it only helps when your ADPP actually contains visit information.

strat_var

One or more columns whose combination defines the table rows (stratification). Default: c("TRT01A", "PARAM") – statistics are separated by treatment arm and parameter. Add e.g. "PCSPEC" to also split by specimen. 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".

param_filter

Optional character vector of PARAM values to keep. NULL (default) keeps every parameter.

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", "Mean", "SD", "CV_pct", "GeoMean", "GeoCV_pct", "Median", "Min", "Max"). NULL (default) shows all of them. Names not produced by this table are ignored.

Value

Named list of data frames with one column per strat_var followed by n, Mean, SD, CV_pct, Median, Min, Max. Use t_pkpt03_col() instead if geometric mean statistics are needed.

Examples

if (FALSE) { # \dontrun{
adpp <- export_cdisc(res_nca)$adpp
tables <- t_pkpt08_uri(adpp)
} # }