Laboratory Test Results and Change from Baseline by Visit

Roche LBT01

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Setup

# Load libraries & data -------------------------------------
library(gtsummary)
library(dplyr)
library(crane)

adsl <- pharmaverseadam::adsl
adlb <- pharmaverseadam::adlb

# Pre-processing --------------------------------------------
data <- adlb |>
  dplyr::filter(
    SAFFL == "Y", # safety population
    PARAMCD %in% c("ALT", "BILI", "CREAT")
    # This step can be used to filter for valid visits. Since the table creation
    # code specifies the visits, we can omit that step here.
  )

Build Table

tbl <- data |>
  filter(
    AVISIT %in% c("Baseline", "Week 4") # specify visits to display in table
  ) |>
  # apply tbl_baseline_chg function to each level of PARAM in the data
  gtsummary::tbl_strata_nested_stack(
    strata = PARAM,
    ~ .x |>
      crane::tbl_baseline_chg(
        baseline_level = "Baseline",
        by = "TRT01A",
        # this dataset has a treatment level called "Screen Failure".
        # Filtering this out as adsl is used to calculate the denominator.
        denominator = adsl |> filter(TRT01A != "Screen Failure")
      )
  ) |>
  # bold lab test labels
  gtsummary::modify_bold(columns = label, rows = tbl_indent_id1 > 0L) |>
  # update header labels
  gtsummary::modify_header(label = "**Lab  \n\U00A0\U00A0\U00A0\U00A0 Visit**") |>
  gtsummary::modify_spanning_header(gtsummary::all_stat_cols() ~ "**{level}**  \nN = {n}")

tbl

Build ARD

# Extract ARD from previously created gtsummary table (refer to "Build Table")
ard <- gather_ard(tbl)

# Output ARD
ard

$`PARAM="Alanine Aminotransferase (U/L)"`
$`PARAM="Alanine Aminotransferase (U/L)"`$tbl_baseline_chg

{cards} data frame: 108 x 12

   group1 group1_level variable variable_level context stat_name stat_label   stat fmt_fun warning error gts_column
1  TRT01A      Placebo     AVAL       Baseline summary      mean       Mean  17.57    <fn>                   stat_1
2  TRT01A      Placebo     AVAL       Baseline summary        sd         SD  9.216    <fn>                   stat_1
3  TRT01A      Placebo     AVAL       Baseline summary    median     Median     15    <fn>                   stat_1
4  TRT01A      Placebo     AVAL       Baseline summary       min        Min      7    <fn>                   stat_1
5  TRT01A      Placebo     AVAL       Baseline summary       max        Max     69    <fn>                   stat_1
6  TRT01A      Placebo     AVAL         Week 4 summary      mean       Mean 18.658    <fn>                   stat_1
7  TRT01A      Placebo     AVAL         Week 4 summary        sd         SD 12.908    <fn>                   stat_1
8  TRT01A      Placebo     AVAL         Week 4 summary    median     Median     16    <fn>                   stat_1
9  TRT01A      Placebo     AVAL         Week 4 summary       min        Min      6    <fn>                   stat_1
10 TRT01A      Placebo     AVAL         Week 4 summary       max        Max    107    <fn>                   stat_1

ℹ 98 more rows

ℹ Use `print(n = ...)` to see more rows

$`PARAM="Bilirubin (umol/L)"`
$`PARAM="Bilirubin (umol/L)"`$tbl_baseline_chg

{cards} data frame: 108 x 12

   group1 group1_level variable variable_level context stat_name stat_label   stat fmt_fun warning error gts_column
1  TRT01A      Placebo     AVAL       Baseline summary      mean       Mean  9.703    <fn>                   stat_1
2  TRT01A      Placebo     AVAL       Baseline summary        sd         SD  3.965    <fn>                   stat_1
3  TRT01A      Placebo     AVAL       Baseline summary    median     Median   8.55    <fn>                   stat_1
4  TRT01A      Placebo     AVAL       Baseline summary       min        Min   5.13    <fn>                   stat_1
5  TRT01A      Placebo     AVAL       Baseline summary       max        Max  25.65    <fn>                   stat_1
6  TRT01A      Placebo     AVAL         Week 4 summary      mean       Mean 11.126    <fn>                   stat_1
7  TRT01A      Placebo     AVAL         Week 4 summary        sd         SD  13.57    <fn>                   stat_1
8  TRT01A      Placebo     AVAL         Week 4 summary    median     Median   8.55    <fn>                   stat_1
9  TRT01A      Placebo     AVAL         Week 4 summary       min        Min   5.13    <fn>                   stat_1
10 TRT01A      Placebo     AVAL         Week 4 summary       max        Max 124.83    <fn>                   stat_1

ℹ 98 more rows
ℹ Use `print(n = ...)` to see more rows

$`PARAM="Creatinine (umol/L)"`
$`PARAM="Creatinine (umol/L)"`$tbl_baseline_chg

{cards} data frame: 108 x 12

   group1 group1_level variable variable_level context stat_name stat_label   stat fmt_fun warning error gts_column
1  TRT01A      Placebo     AVAL       Baseline summary      mean       Mean 97.651    <fn>                   stat_1
2  TRT01A      Placebo     AVAL       Baseline summary        sd         SD 17.779    <fn>                   stat_1
3  TRT01A      Placebo     AVAL       Baseline summary    median     Median  97.24    <fn>                   stat_1
4  TRT01A      Placebo     AVAL       Baseline summary       min        Min  61.88    <fn>                   stat_1
5  TRT01A      Placebo     AVAL       Baseline summary       max        Max 159.12    <fn>                   stat_1
6  TRT01A      Placebo     AVAL         Week 4 summary      mean       Mean 98.641    <fn>                   stat_1
7  TRT01A      Placebo     AVAL         Week 4 summary        sd         SD 18.557    <fn>                   stat_1
8  TRT01A      Placebo     AVAL         Week 4 summary    median     Median  97.24    <fn>                   stat_1
9  TRT01A      Placebo     AVAL         Week 4 summary       min        Min  70.72    <fn>                   stat_1
10 TRT01A      Placebo     AVAL         Week 4 summary       max        Max  176.8    <fn>                   stat_1

ℹ 98 more rows
ℹ Use `print(n = ...)` to see more rows