Package 'crane'

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()

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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:

• Default summary type for continuous variables is 'continuous2'.

• Number of non-missing observations is added for each variable by default and placed on the row under the header.

• The ⁠tbl_summary(missing*)⁠ arguments have been renamed to ⁠tbl_demographics(nonmissing*)⁠ with updated default values.

• The default footnotes from tbl_summary() are removed.

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

• Calls the gtsummary::theme_gtsummary_compact() theme.

• Uses label_roche_pvalue() as the default formatting function for all p-values.

• Defaults to a mono-spaced font for gt 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()

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