[R] How to extract table results from survival summary object

[David L Carlson]

This will create a data.frame containing the results of the summary(mod) object. You can find out what that is using the command ?summary.survfit. You have an error in your example since death is not a variable in lung:

> library(survival)
> data(lung)
> mod <- with(lung, survfit(Surv(time, status)~ 1))
> res <- summary(mod)
> str(res)
List of 14
 $ n        : int 228
 $ time     : num [1:139] 5 11 12 13 15 26 30 31 53 54 ...
 $ n.risk   : num [1:139] 228 227 224 223 221 220 219 218 217 215 ...
 $ n.event  : num [1:139] 1 3 1 2 1 1 1 1 2 1 ...
 $ n.censor : num [1:139] 0 0 0 0 0 0 0 0 0 0 ...
 $ surv     : num [1:139] 0.996 0.982 0.978 0.969 0.965 ...
 $ type     : chr "right"
 $ std.err  : num [1:139] 0.00438 0.00869 0.0097 0.01142 0.01219 ...
 $ upper    : num [1:139] 1 1 0.997 0.992 0.989 ...
 $ lower    : num [1:139] 0.987 0.966 0.959 0.947 0.941 ...
 $ conf.type: chr "log"
 $ conf.int : num 0.95
 $ call     : language survfit(formula = Surv(time, status) ~ 1)
 $ table    : Named num [1:7] 228 228 228 165 310 285 363
  ..- attr(*, "names")= chr [1:7] "records" "n.max" "n.start" "events" ...
 - attr(*, "class")= chr "summary.survfit"
> # Extract the columns you want
> cols <- lapply(c(2:6, 8:10) , function(x) res[x])
> # Combine the columns into a data frame
> tbl <- do.call(data.frame, cols)
> str(tbl)
'data.frame':   139 obs. of  8 variables:
 $ time    : num  5 11 12 13 15 26 30 31 53 54 ...
 $ n.risk  : num  228 227 224 223 221 220 219 218 217 215 ...
 $ n.event : num  1 3 1 2 1 1 1 1 2 1 ...
 $ n.censor: num  0 0 0 0 0 0 0 0 0 0 ...
 $ surv    : num  0.996 0.982 0.978 0.969 0.965 ...
 $ std.err : num  0.00438 0.00869 0.0097 0.01142 0.01219 ...
 $ upper   : num  1 1 0.997 0.992 0.989 ...
 $ lower   : num  0.987 0.966 0.959 0.947 0.941 ...

Since res is a list containing the columns you want plus other information, we need to extract the needed columns from res and then combine those columns into a data.frame.

-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Juan Andres Hernandez
Sent: Tuesday, October 7, 2014 8:41 AM
To: r-help at r-project.org
Subject: [R] How to extract table results from survival summary object

Hi. I need to extract the "matrix" or "data.frame" results from a survival
object.

library(survival)
data(lung)
mod=with(lung, survfit(Surv(time,death)~ 1))
res=summary(mod)

res show in consola the "matrix" I am looking for, but I can't find the way
to save or assign this table to an object. Anyone knows how to solve it.
Thank's in advance

Juan A. Hernández

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