add_p.tbl_survfit: Adds p-value to survfit table

View source: R/add_p.R

add_p.tbl_survfitR Documentation

Adds p-value to survfit table

Description

\lifecycle

maturing Calculate and add a p-value

Usage

## S3 method for class 'tbl_survfit'
add_p(
  x,
  test = "logrank",
  test.args = NULL,
  pvalue_fun = style_pvalue,
  include = everything(),
  quiet = NULL,
  ...
)

Arguments

x

Object of class "tbl_survfit"

test

string indicating test to use. Must be one of "logrank", "tarone", "survdiff", "petopeto_gehanwilcoxon", "coxph_lrt", "coxph_wald", "coxph_score". See details below

test.args

List of formulas containing additional arguments to pass to tests that accept arguments. For example, add an argument for all t-tests, use test.args = all_tests("t.test") ~ list(var.equal = TRUE)

pvalue_fun

Function to round and format p-values. Default is style_pvalue. The function must have a numeric vector input (the numeric, exact p-value), and return a string that is the rounded/formatted p-value (e.g. pvalue_fun = function(x) style_pvalue(x, digits = 2) or equivalently, purrr::partial(style_pvalue, digits = 2)).

include

Variables to include in output. Input may be a vector of quoted variable names, unquoted variable names, or tidyselect select helper functions. Default is everything().

quiet

Logical indicating whether to print messages in console. Default is FALSE

...

Not used

test argument

The most common way to specify test= is by using a single string indicating the test name. However, if you need to specify different tests within the same table, the input in flexible using the list notation common throughout the gtsummary package. For example, the following code would call the log-rank test, and a second test of the G-rho family.

... %>%
  add_p(test = list(trt ~ "logrank", grade ~ "survdiff"),
        test.args = grade ~ list(rho = 0.5))

Example Output

Example 1

image of rendered example table

Example 2

image of rendered example table

See Also

Other tbl_survfit tools: add_n.tbl_survfit(), add_nevent.tbl_survfit(), modify, tbl_merge(), tbl_split(), tbl_stack(), tbl_strata(), tbl_survfit()

Examples



library(survival)

gts_survfit <-
  list(
    survfit(Surv(ttdeath, death) ~ grade, trial),
    survfit(Surv(ttdeath, death) ~ trt, trial)
  ) %>%
  tbl_survfit(times = c(12, 24))

# Example 1 ----------------------------------
add_p_tbl_survfit_ex1 <-
  gts_survfit %>%
  add_p()

# Example 2 ----------------------------------
# Pass `rho=` argument to `survdiff()`
add_p_tbl_survfit_ex2 <-
  gts_survfit %>%
  add_p(test = "survdiff", test.args = list(rho = 0.5))



gtsummary documentation built on Jan. 13, 2023, 9:10 a.m.