This function creates a listing of pharmacokinetic (PK) concentration data segregating a dataset in lists that are customizable in title, footnotes, grouping/displayed variables, missing/zero values and/or number of digits displayed.
Usage
l_pkconc(
data,
listgroup_vars = c("PARAM", "PCSPEC", "ROUTE"),
grouping_vars = c("TRT01A", "USUBJID", "AVISIT"),
displaying_vars = c("NFRLT", "AFRLT", "AVAL"),
formatting_vars_table = NULL,
title = paste0("Listing of PK Concentration by Treatment Group,",
"Subject and Nominal Time, PK Population"),
subtitle = NULL,
footnote = "*: Patients excluded from the summary table and mean plots"
)Arguments
- data
A data frame containing the PK concentration data.
- listgroup_vars
A character vector specifying the variables to separate lists.
- grouping_vars
A character vector specifying the grouping variables within each list.
- displaying_vars
A character vector specifying the variables to display in the listing.
- formatting_vars_table
A data frame with the formatting of each variable. See details.
- title
A character string to parse specifying the main title for the entire listing.
- subtitle
A character string to parse specifying the subtitle to use for each list.
- footnote
A character string to parse specifying the footnote of the listing table.
Details
The function performs the following steps:
Groups the data based on the specified grouping variables.
Formats the 0 and NA values as defined by the formatting table.
Creates a listing for each unique combination of the grouping variables.
The formatting_vars_table should be a data frame with the following columns:
var_name: The name of the variable.Label: The label for the variable.na_str: The string to use for NA values.zero_str: The string to use for 0 values.align: The alignment for the variable (e.g., "center").format_fun: The formatting function to use ("round" or "signif").digits: The number of digits to use for numeric formatting.
Examples
# Create a sample dataframe 'data' with the required variables
set.seed(123)
data <- data.frame(
PARAM = rep(c("Param1", "Param2"), each = 6),
PCSPEC = rep(c("Blood", "Urine"), each = 6),
TRT01A = rep(c("Treatment1", "Treatment2"), each = 6),
USUBJID = rep(c(rep(1, 3), rep(2, 3)), 2),
NFRLT = rep(1:3, 4),
AFRLT = rep(1:3, 4) + runif(12, 0, 0.5),
TIMEU = "hours",
AVAL = rep(0:2, 4) + runif(12, 0, 0.5),
AVALU = "mg/L"
)
# Define the formatting table
formatting_vars_table <- data.frame(var_name = names(data),
Label = c("Parameter", "Specimen", "Treatment Arm",
"Unique Subject ID", "Norminal Time ($TIMEU)",
"Actual Time ($TIMEU)", "Time Unit",
"Analyte Value ($AVALU)", "Analyte Unit"),
na_str = "Missing",
zero_str = c(rep("0", 7), "BLQ", "0"),
align = "center",
format_fun = c(NA, NA, NA, NA,
"round", "round", NA, "round", NA),
digits = c(NA, NA, NA, NA, 2, 2, NA, 3, NA))
# Call the l_pkconc function with the sample data
listing_ex <- l_pkconc(data = data,
listgroup_vars = c("PARAM", "PCSPEC"),
grouping_vars = c("TRT01A", "USUBJID"),
displaying_vars = c("NFRLT", "AFRLT", "AVAL"),
formatting_vars_table = formatting_vars_table,
title = "Listing of PK Concentration",
subtitle = "Patients with !PARAM: $PARAM (!PCSPEC: $PCSPEC)"
)
print(listing_ex)
#> $Param1.Blood
#> Listing of PK Concentration
#> Patients with Parameter: Param1 (Specimen: Blood)
#>
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#> Treatment Arm Unique Subject ID Norminal Time (hours) Actual Time (hours) Analyte Value (mg/L)
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#> Treatment1 1 1 1.14 0.339
#> 2 2.39 1.286
#> 3 3.2 2.051
#> 2 1 1.44 0.45
#> 2 2.47 1.123
#> 3 3.02 2.021
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> *: Patients excluded from the summary table and mean plots
#>
#> $Param2.Urine
#> Listing of PK Concentration
#> Patients with Parameter: Param2 (Specimen: Urine)
#>
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#> Treatment Arm Unique Subject ID Norminal Time (hours) Actual Time (hours) Analyte Value (mg/L)
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#> Treatment2 1 1 1.26 0.164
#> 2 2.45 1.477
#> 3 3.28 2.445
#> 2 1 1.23 0.346
#> 2 2.48 1.32
#> 3 3.23 2.497
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> *: Patients excluded from the summary table and mean plots
#>