gtsummary: inline_text.tbl_survfit – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

inline_text.tbl_survfit

Report statistics from survfit tables inline

Description

Extracts and returns statistics from a tbl_survfit object for inline reporting in an R markdown document. Detailed examples in the inline_text vignette

Usage

## S3 method for class 'tbl_survfit'
inline_text(
  x,
  variable = NULL,
  level = NULL,
  pattern = NULL,
  time = NULL,
  prob = NULL,
  column = NULL,
  estimate_fun = x$inputs$estimate_fun,
  pvalue_fun = NULL,
  ...
)

Arguments

`x`	Object created from tbl_survfit
`variable`	Variable name of statistic to present.
`level`	Level of the variable to display for categorical variables. Can also specify the 'Unknown' row. Default is `NULL`
`pattern`	String indicating the statistics to return.
`time`	time for which to return survival probabilities.
`prob`	probability with values in (0,1)
`column`	column to print from `x$table_body`. Columns may be selected with `time=` or `prob=` as well.
`estimate_fun`	Function to round and format estimate and confidence limits. Default is the same function used in `tbl_survfit()`
`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)`).
`...`	Not used

Value

A string reporting results from a gtsummary table

Author(s)

Daniel D. Sjoberg

Examples

library(survival)
# fit survfit
fit1 <- survfit(Surv(ttdeath, death) ~ trt, trial)
fit2 <- survfit(Surv(ttdeath, death) ~ 1, trial)

# sumarize survfit objects
tbl1 <-
  tbl_survfit(
    fit1,
    times = c(12, 24),
    label = "Treatment",
    label_header = "**{time} Month**"
  ) %>%
  add_p()

tbl2 <-
  tbl_survfit(
    fit2,
    probs = 0.5,
    label_header = "**Median Survival**"
  )

# report results inline
inline_text(tbl1, time = 24, level = "Drug B")
inline_text(tbl1, column = p.value)
inline_text(tbl2, prob = 0.5)

gtsummary

Presentation-Ready Data Summary and Analytic Result Tables

v1.4.0

MIT + file LICENSE

Authors

Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Joseph Larmarange [aut] (<https://orcid.org/0000-0001-7097-700X>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>), Jessica Lavery [ctb] (<https://orcid.org/0000-0002-2746-5647>), Stephanie Lobaugh [ctb], Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)

Initial release