Create an lt table from a design summary

S3 methods for lt() that convert fixed or group sequential design summaries into formatted lt tables.

Usage

# S3 method for class 'fixed_design_summary'
lt(data, title = NULL, footnote = NULL, ...)

# S3 method for class 'gs_design_summary'
lt(
  data,
  title = NULL,
  subtitle = NULL,
  colname_spanner = "Cumulative boundary crossing probability",
  colname_spannersub = c("Alternate hypothesis", "Null hypothesis"),
  footnote = NULL,
  display_bound = c("Efficacy", "Futility", "Harm"),
  display_columns = NULL,
  display_inf_bound = FALSE,
  ...
)

Arguments

data

A summary object of a fixed or group sequential design.

title

A string to specify the title of the table.

footnote

A list containing content, location, and attr. content is a vector of string to specify the footnote text; location is a vector of string to specify the locations to put the superscript of the footnote index; attr is a vector of string to specify the attributes of the footnotes, for example, c("colname", "title", "subtitle", "analysis", "spanner"). To disable footnotes, use footnote = FALSE.

...

Additional arguments (not used).

subtitle

A string to specify the subtitle of the table.

colname_spanner

A string to specify the spanner of the table.

colname_spannersub

A vector of strings to specify the spanner details of the table.

display_bound

A vector of strings specifying the label of the bounds. The default is c("Efficacy", "Futility", "Harm").

display_columns

A vector of strings specifying the variables to be displayed in the summary table.

display_inf_bound

Logical, whether to display the +/-inf bound.

Value

An lt_tbl object.

Examples

# Fixed design examples ----

# Enrollment rate
enroll_rate <- define_enroll_rate(
  duration = 18,
  rate = 20
)

# Failure rates
fail_rate <- define_fail_rate(
  duration = c(4, 100),
  fail_rate = log(2) / 12,
  dropout_rate = .001,
  hr = c(1, .6)
)

# Study duration in months
study_duration <- 36

# Experimental / Control randomization ratio
ratio <- 1

# 1-sided Type I error
alpha <- 0.025

# Type II error (1 - power)
beta <- 0.1

# Example 1 ----
fixed_design_ahr(
  alpha = alpha, power = 1 - beta,
  enroll_rate = enroll_rate, fail_rate = fail_rate,
  study_duration = study_duration, ratio = ratio
) |>
  summary() |>
  lt()

# Example 2 ----
fixed_design_fh(
  alpha = alpha, power = 1 - beta,
  enroll_rate = enroll_rate, fail_rate = fail_rate,
  study_duration = study_duration, ratio = ratio
) |>
  summary() |>
  lt()
# \donttest{
# Group sequential design examples ---

# Example 1 ----
# The default output

gs_design_ahr() |>
  summary() |>
  lt()

gs_power_ahr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt()

gs_design_wlr() |>
  summary() |>
  lt()

gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt()

gs_power_combo() |>
  summary() |>
  lt()

gs_design_rd() |>
  summary() |>
  lt()

gs_power_rd() |>
  summary() |>
  lt()

# Example 2 ----
# Usage of title = ..., subtitle = ...
# to edit the title/subtitle
gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt(
    title = "Bound Summary",
    subtitle = "from gs_power_wlr"
  )

# Example 3 ----
# Usage of colname_spanner = ..., colname_spannersub = ...
# to edit the spanner and its sub-spanner
gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt(
    colname_spanner = "Cumulative probability to cross boundaries",
    colname_spannersub = c("under H1", "under H0")
  )

# Example 4 ----
# Usage of footnote = ...
# to edit the footnote
gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt(
    footnote = list(
      content = c(
        "approximate weighted hazard ratio to cross bound.",
        "wAHR is the weighted AHR.",
        "the crossing probability.",
        "this table is generated by gs_power_wlr."
      ),
      location = c("~wHR at bound", NA, NA, NA),
      attr = c("colname", "analysis", "spanner", "title")
    )
  )

# Example 5 ----
# Usage of display_bound = ...
# to either show efficacy bound or futility bound, or both(default)
gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt(display_bound = "Efficacy")

# Example 6 ----
# Usage of display_columns = ...
# to select the columns to display in the summary table
gs_power_wlr(lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.1)) |>
  summary() |>
  lt(display_columns = c("Analysis", "Bound", "Nominal p", "Z", "Probability"))
# }