[R] Extracting results from a function output

[R. Michael Weylandt]

Assuming I'm reading your post correctly -- fit is the output object
and the lines following >fit are the console output, which implicitly
calls print -- it looks like the median isn't stored in fit but is
calculated on the fly in the print call. But this doesn't seem
consistent with your claim that:

"Print" function does not reveal them either.

Could you perhaps clarify your statement about print(fit)?

Cheers from Princeton!

Michael Weylandt

On Mon, Oct 17, 2011 at 11:13 AM, Cem Girit <girit at biopticon.com> wrote:
> Hello,
>
> I am having hard time obtaining a value from a function. "fit" is a survival
> function that produces some results, such as "median", "confidence
> intervals" etc. But str() function does not list these values. How can I
> extract these to be able use them? For example, I need "median" value for
> the group DrugA which is 48. "Print" function does not reveal them either.
>
> Thank you.
>
>> fit
> Call: survfit(formula = Surv(tT, dT) ~ gT, conf.type = "log-log")
>
> records n.max n.start events median 0.95LCL 0.95UCL
> gT=DrugA 9 9 9 6 48 32 NA
> gT=DrugB 9 9 9 3 NA 42 NA
> gT=DrugC 9 9 9 4 NA 42 NA
> gT=Vehicle 9 9 9 8 40 37 45
>
>> str(fit)
> List of 14
> $ n : int [1:4] 9 9 9 9
> $ time : num [1:28] 32 43 45 46 48 54 55 60 62 42 ...
> $ n.risk : num [1:28] 9 8 7 6 5 4 3 2 1 9 ...
> $ n.event : num [1:28] 1 1 1 1 1 0 1 0 0 2 ...
> $ n.censor : num [1:28] 0 0 0 0 0 1 0 1 1 0 ...
> $ surv : num [1:28] 0.889 0.778 0.667 0.556 0.444 ...
> $ type : chr "right"
> $ strata : Named int [1:4] 9 6 6 7
> ..- attr(*, "names")= chr [1:4] "gT=DrugA" "gT=DrugB" "gT=DrugC"
> "gT=Vehicle"
> $ std.err : num [1:28] 0.118 0.178 0.236 0.298 0.373 ...
> $ upper : num [1:28] 0.984 0.939 0.878 0.805 0.719 ...
> $ lower : num [1:28] 0.433 0.365 0.282 0.204 0.136 ...
> $ conf.type: chr "log-log"
> $ conf.int : num 0.95
> $ call : language survfit(formula = Surv(tT, dT) ~ gT, conf.type =
> "log-log")
> - attr(*, "class")= chr "survfit"
>
>
>
> Cem
>
>
>
> Cem Girit, PhD
>
>
>
> Biopticon Corporation
>
> 182 Nassau Street, Suite 204
>
> Princeton, NJ 08542
>
> Tel: (609)-853-0231
>
> Email:  <mailto:cgirit at biopticon.com> girit at biopticon.com
>
>
>
> This email message and any attachments are confidential ...{{dropped:14}}
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>