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Title: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
Version: 0.1.0
Description: Tables summarizing clinical trial results are often complex and require detailed tailoring prior to submission to a health authority. The 'crane' package supplements the functionality of the 'gtsummary' package for creating these often highly bespoke tables in the pharmaceutical industry.
License: Apache License 2.0
URL: https://github.com/insightsengineering/crane, https://insightsengineering.github.io/crane/
BugReports: https://github.com/insightsengineering/crane/issues
Depends: R (≥ 4.2)
Imports: cli (≥ 3.6.4), dplyr (≥ 1.1.4), flextable (≥ 0.9.7), gt (≥ 0.11.1), gtsummary (≥ 2.1.0), rlang (≥ 1.1.5)
Suggests: testthat (≥ 3.0.0)
Config/Needs/check: hms
Config/Needs/website: rmarkdown, yaml, insightsengineering/nesttemplate
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-02-21 22:53:07 UTC; sjobergd
Author: Daniel D. Sjoberg ORCID iD [aut, cre], Emily de la Rua [aut], Davide Garolini [aut], Abinaya Yogasekaram [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-24 17:00:07 UTC

crane: Supplements the 'gtsummary' Package for Pharmaceutical Reporting

Description

Tables summarizing clinical trial results are often complex and require detailed tailoring prior to submission to a health authority. The 'crane' package supplements the functionality of the 'gtsummary' package for creating these often highly bespoke tables in the pharmaceutical industry.

Author(s)

Maintainer: Daniel D. Sjoberg danield.sjoberg@gmail.com (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Add Blank Row

Description

Add a blank row below each variable group. A blank row will not be added to the bottom of the table.

NOTE: For HTML flextable output (which includes the RStudio IDE Viewer), the blank rows do not render. But they will appear when the table is rendered to Word.

Usage

add_blank_row(x)

Arguments

x

(gtsummary)
a 'gtsummary' table. The table must include a column named 'variable' in x$table_body.

Value

updated 'gtsummary' table

Examples

gtsummary::trial |>
  tbl_demographics(
    by = trt,
    include = c(age, marker, grade)
  ) |>
  add_blank_row()

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

dplyr

%>%

gtsummary

all_categorical, all_continuous

Round p-values

Description

Round p-values

Usage

roche_pvalue(
  x,
  big.mark = ifelse(decimal.mark == ",", " ", ","),
  decimal.mark = getOption("OutDec"),
  ...
)

label_roche_pvalue(
  big.mark = ifelse(decimal.mark == ",", " ", ","),
  decimal.mark = getOption("OutDec"),
  ...
)

Arguments

x

(numeric)
Numeric vector of p-values.

big.mark

(string)
Character used between every 3 digits to separate hundreds/thousands/millions/etc. Default is ",", except when decimal.mark = "," when the default is a space.

decimal.mark

(string)
The character to be used to indicate the numeric decimal point. Default is "." or getOption("OutDec")

...

Arguments passed on to base::format()

Value

A character vector of rounded p-values

Examples

x <- c(0.0000001, 0.123456)

roche_pvalue(x)
label_roche_pvalue()(x)

Demographics Table

Description

This is a thin wrapper of gtsummary::tbl_summary() with the following differences:

Usage

tbl_demographics(
  data,
  by = NULL,
  label = NULL,
  statistic = list(all_continuous() ~ c("{mean} ({sd})", "{median}", "{min} - {max}"),
    all_categorical() ~ "{n} ({p}%)"),
  digits = NULL,
  type = NULL,
  value = NULL,
  nonmissing = c("always", "ifany", "no"),
  nonmissing_text = "n",
  nonmissing_stat = "{N_nonmiss}",
  sort = all_categorical(FALSE) ~ "alphanumeric",
  percent = c("column", "row", "cell"),
  include = everything()
)

Arguments

data

(data.frame)
A data frame.

by

(tidy-select)
A single column from data. Summary statistics will be stratified by this variable. Default is NULL.

label

(formula-list-selector)
Used to override default labels in summary table, e.g. list(age = "Age, years"). The default for each variable is the column label attribute, attr(., 'label'). If no label has been set, the column name is used.

statistic

(formula-list-selector)
Specifies summary statistics to display for each variable. The default is list(all_continuous() ~ "{median} ({p25}, {p75})", all_categorical() ~ "{n} ({p}%)"). See below for details.

digits

(formula-list-selector)
Specifies how summary statistics are rounded. Values may be either integer(s) or function(s). If not specified, default formatting is assigned via assign_summary_digits(). See below for details.

type

(formula-list-selector)
Specifies the summary type. Accepted value are c("continuous", "continuous2", "categorical", "dichotomous"). If not specified, default type is assigned via assign_summary_type(). See below for details.

value

(formula-list-selector)
Specifies the level of a variable to display on a single row. The gtsummary type selectors, e.g. all_dichotomous(), cannot be used with this argument. Default is NULL. See below for details.

nonmissing, nonmissing_text, nonmissing_stat

Arguments dictating how and if missing values are presented:

  • nonmissing: must be one of c("always", "ifany", "no")

  • nonmissing_text: string indicating text shown on non-missing row. Default is "n"

  • nonmissing_stat: statistic to show on non-missing row. Default is "{N_nonmiss}". Possible values are N_nonmiss, N_miss, N_obs,, p_nonmiss p_miss.

sort

(formula-list-selector)
Specifies sorting to perform for categorical variables. Values must be one of c("alphanumeric", "frequency"). Default is all_categorical(FALSE) ~ "alphanumeric".

percent

(string)
Indicates the type of percentage to return. Must be one of c("column", "row", "cell"). Default is "column".

include

(tidy-select)
Variables to include in the summary table. Default is everything().

Value

a 'gtsummary' table

Examples

# Example 1 ----------------------------------
gtsummary::trial |>
  tbl_demographics(
    by = trt,
    include = c(age, grade)
  )

Roche Theme

Description

A gtsummary theme for Roche tables

Usage

theme_gtsummary_roche(set_theme = TRUE, font_size = NULL)

Arguments

set_theme

(scalar logical)
Logical indicating whether to set the theme. Default is TRUE. When FALSE the named list of theme elements is returned invisibly

font_size

(scalar numeric)
Numeric font size for compact theme. Default is 13 for gt tables, and 8 for all other output types

Value

theme list

Examples

theme_gtsummary_roche()

tbl_demographics(gtsummary::trial, by = trt, include = c(age, grade))

gtsummary::reset_gtsummary_theme()

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.