st_sum: Summarize survival-time data

In emilelatour/lamisc: Latour's Little Helpers

Summarize survival-time data

Description

An R flavored version of the Stata command stsum. Presents summary statistics: time at risk; incidence rate; number of subjects; and the 25th, 50th, and 75th percentiles of survival time.

Usage

st_sum(data, time, event, type = "right", group)

Arguments

data	A data frame
time	For right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.
event	The status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death). For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored. For multiple enpoint data the event variable will be a factor, whose first level is treated as censoring. Although unusual, the event indicator can be omitted, in which case all subjects are assumed to have an event.
type	character string specifying the type of censoring. Possible values are "right", "left", "counting", "interval", "interval2" or "mstate".
group	Variable name (unquoted) to stratify on

Value

A list

References

https://www.stata.com/manuals13/ststsum.pdf

Examples

#### Example 1 --------------------------------

library(dplyr)
library(tibble)
page_2 <- tibble::tribble(
  ~group, ~time, ~dead, ~st, ~d, ~t, ~t0,
  1,   143,     1,    1,   1, 143,    0,
  1,   164,     1,    1,   1, 164,    0,
  1,   188,     1,    1,   1, 188,    0,
  1,   188,     1,    1,   1, 188,    0,
  1,   190,     1,    1,   1, 190,    0,
  1,   192,     1,    1,   1, 192,    0,
  1,   206,     1,    1,   1, 206,    0,
  1,   209,     1,    1,   1, 209,    0,
  1,   213,     1,    1,   1, 213,    0,
  1,   216,     1,    1,   1, 216,    0,
  1,   220,     1,    1,   1, 220,    0,
  1,   227,     1,    1,   1, 227,    0,
  1,   230,     1,    1,   1, 230,    0,
  1,   234,     1,    1,   1, 234,    0,
  1,   246,     1,    1,   1, 246,    0,
  1,   265,     1,    1,   1, 265,    0,
  1,   304,     1,    1,   1, 304,    0,
  1,   216,     0,    1,   0, 216,    0,
  1,   244,     0,    1,   0, 244,    0,
  2,   142,     1,    1,   1, 142,    0,
  2,   156,     1,    1,   1, 156,    0,
  2,   163,     1,    1,   1, 163,    0,
  2,   198,     1,    1,   1, 198,    0,
  2,   205,     1,    1,   1, 205,    0,
  2,   232,     1,    1,   1, 232,    0,
  2,   232,     1,    1,   1, 232,    0,
  2,   233,     1,    1,   1, 233,    0,
  2,   233,     1,    1,   1, 233,    0,
  2,   233,     1,    1,   1, 233,    0,
  2,   233,     1,    1,   1, 233,    0,
  2,   239,     1,    1,   1, 239,    0,
  2,   240,     1,    1,   1, 240,    0,
  2,   261,     1,    1,   1, 261,    0,
  2,   280,     1,    1,   1, 280,    0,
  2,   280,     1,    1,   1, 280,    0,
  2,   296,     1,    1,   1, 296,    0,
  2,   296,     1,    1,   1, 296,    0,
  2,   323,     1,    1,   1, 323,    0,
  2,   204,     0,    1,   0, 204,    0,
  2,   344,     0,    1,   0, 344,    0
)


st_sum(data = page_2,
       time = time,
       event = dead,
       group = group)

#### Example 2 --------------------------------

sample_df <- tibble::tribble(
  ~exp, ~time, ~disease, ~st, ~d, ~t, ~t0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     1,        1,    1,   1,   1,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     2,        1,    1,   1,   2,    0,
     0,     3,        1,    1,   1,   3,    0,
     0,     3,        1,    1,   1,   3,    0,
     0,     4,        0,    1,   0,   4,    0,
     0,     5,        0,    1,   0,   5,    0,
     0,     5,        0,    1,   0,   5,    0,
     0,     5,        1,    1,   1,   5,    0,
     0,     6,        0,    1,   0,   6,    0,
     0,     7,        0,    1,   0,   7,    0,
     0,     7,        0,    1,   0,   7,    0,
     0,     8,        0,    1,   0,   8,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     1,        1,    1,   1,   1,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     2,        1,    1,   1,   2,    0,
     1,     3,        1,    1,   1,   3,    0,
     1,     3,        1,    1,   1,   3,    0,
     1,     4,        0,    1,   0,   4,    0,
     1,     4,        0,    1,   0,   4,    0,
     1,     4,        0,    1,   0,   4,    0,
     1,     4,        0,    1,   0,   4,    0,
     1,     4,        1,    1,   1,   4,    0,
     1,     5,        0,    1,   0,   5,    0,
     1,     5,        0,    1,   0,   5,    0,
     1,     6,        0,    1,   0,   6,    0,
     1,     6,        0,    1,   0,   6,    0,
     1,    10,        0,    1,   0,  10,    0,
     1,    12,        0,    1,   0,  12,    0
  )


st_sum(data = sample_df,
       time = time,
       event = disease,
       group = exp)


st_sum(data = sample_df,
       time = time,
       event = (disease == 1),
       group = exp)

emilelatour/lamisc documentation built on April 9, 2024, 10:33 a.m.