tbl_shift: Shift Table

In crane: Supplements the 'gtsummary' Package for Pharmaceutical Reporting

Shift Table

Description

Typical use is tabulating post-baseline measurement stratified by the baseline measurement.

Usage

tbl_shift(
  data,
  variable,
  strata = NULL,
  by = NULL,
  data_header = NULL,
  strata_location = c("new_column", "header"),
  strata_label = "{strata}",
  header = "{level}  \nN = {n}",
  label = NULL,
  nonmissing = "always",
  nonmissing_text = "Total",
  ...
)

## S3 method for class 'tbl_shift'
add_overall(
  x,
  col_label = "All Participants  \n(N = {gtsummary::style_number(n)})",
  last = FALSE,
  ...
)

Arguments

data	(data.frame) A data frame.
variable	(tidy-select) Variable to tabulate. Typically the post-baseline grade.
strata	(tidy-select) Stratifying variable. Typically the baseline grade.
by	(tidy-select) Variable to report results by. Typical value is the treatment arm.
data_header	(data.frame) Data frame used to calculate the Ns in the table header. Only include the columns needed to merge with data: these are typically the 'USUBJID' and the treatment arm only, e.g ADSL[c("USUBJID", "ARM")].
strata_location	(string) Specifies the location where the individual stratum levels will be printed. Must be one of c("new_column", "header"). "new_column": stratum labels are placed in a new column to the left of the tabulated results. "header": stratum labels are placed in a header row above the tabulations.
strata_label	(string) A glue-string that inserts stratum level. Default is '{strata}', and {n} is also available to insert.
header	(string) String that is passed to gtsummary::modify_header(all_stat_cols() ~ header).
label	(formula-list-selector) Used to specify the labels for the strata and variable columns. Default is to use the column label attribute.
nonmissing, nonmissing_text, ...	Argument passed to tbl_roche_summary(). See details below for call details to tbl_roche_summary().
x	(tbl_shift) Object of class 'tbl_shift'.
col_label	(string) String indicating the column label. Default is "All Participants \nN = {gtsummary::style_number(n)}"
last	(scalar logical) Logical indicator to display overall column last in table. Default is FALSE, which will display overall column first.

Details

Broadly, this function is a wrapper for chunk below with some additional calls to ⁠gtsummary::modify_*()⁠ function to update the table's headers, indentation, column alignment, etc.

gtsummary::tbl_strata2(
  data = data,
  strata = strata,
   ~ tbl_roche_summary(.x, include = variable, by = by)
)

Value

a 'gtsummary' table

Examples

library(dplyr, warn.conflicts = FALSE)

# subsetting ADLB on one PARAM, and the highest grade
adlb <- pharmaverseadam::adlb |>
  select("USUBJID", "TRT01A", "PARAM", "PARAMCD", "ATOXGRH", "BTOXGRH", "VISITNUM") |>
  mutate(TRT01A = factor(TRT01A)) |>
  filter(PARAMCD %in% c("CHOLES", "GLUC")) |>
  slice_max(by = c(USUBJID, PARAMCD), order_by = ATOXGRH, n = 1L, with_ties = FALSE) |>
  labelled::set_variable_labels(
    BTOXGRH = "Baseline  \nNCI-CTCAE Grade",
    ATOXGRH = "Post-baseline  \nNCI-CTCAE Grade"
  )
adsl <- pharmaverseadam::adsl[c("USUBJID", "TRT01A")] |>
  filter(TRT01A != "Screen Failure")

# Example 1 ----------------------------------
# tabulate baseline grade by worst grade
tbl_shift(
  data = filter(adlb, PARAMCD %in% "CHOLES"),
  strata = BTOXGRH,
  variable = ATOXGRH,
  by = TRT01A,
  data_header = adsl
)

# Example 2 ----------------------------------
# same as Ex1, but with the stratifying variable levels in header rows
adlb |>
  filter(PARAMCD %in% "CHOLES") |>
  labelled::set_variable_labels(
    BTOXGRH = "Baseline NCI-CTCAE Grade",
    ATOXGRH = "Post-baseline NCI-CTCAE Grade"
  ) |>
  tbl_shift(
    data = ,
    strata = BTOXGRH,
    variable = ATOXGRH,
    strata_location = "header",
    by = TRT01A,
    data_header = adsl
  )

# Example 3 ----------------------------------
# same as Ex2, but with two labs
adlb |>
  labelled::set_variable_labels(
    BTOXGRH = "Baseline NCI-CTCAE Grade",
    ATOXGRH = "Post-baseline NCI-CTCAE Grade"
  ) |>
  tbl_strata_nested_stack(
    strata = PARAM,
    ~ .x |>
      tbl_shift(
        strata = BTOXGRH,
        variable = ATOXGRH,
        strata_location = "header",
        by = TRT01A,
        data_header = adsl
      )
  ) |>
  # Update header with Lab header and indentation (the '\U00A0' character adds whitespace)
  modify_header(
    label = "Lab  \n\U00A0\U00A0\U00A0\U00A0
             Baseline NCI-CTCAE Grade  \n\U00A0\U00A0\U00A0\U00A0\U00A0\U00A0\U00A0\U00A0
             Post-baseline NCI-CTCAE Grade"
  )

# Example 4 ----------------------------------
# Include the treatment variable in a new column
filter(adlb, PARAMCD %in% "CHOLES") |>
  right_join(
    pharmaverseadam::adsl[c("USUBJID", "TRT01A")] |>
      filter(TRT01A != "Screen Failure"),
    by = c("USUBJID", "TRT01A")
  ) |>
  tbl_shift(
    strata = TRT01A,
    variable = BTOXGRH,
    by = ATOXGRH,
    header = "{level}",
    strata_label = "{strata}, N={n}",
    label = list(TRT01A = "Actual Treatment"),
    percent = "cell",
    nonmissing = "no"
  ) |>
  modify_spanning_header(all_stat_cols() ~ "Worst Post-baseline NCI-CTCAE Grade")

crane documentation built on Aug. 30, 2025, 1:12 a.m.