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.> fitCall: 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@biopticon.com> girit@biopticon.com This email message and any attachments are confidential ...{{dropped:14}}
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. >
On Oct 17, 2011, at 11:13 AM, Cem Girit 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.I'm not sure what you mean when you say the "Print" function does not "reveal them". For one thing the function is spelled "print" and for another thing I see the desired "48" in the output. http://tolstoy.newcastle.edu.au/R/e6/help/09/05/15413.html So the answer in your case is: summary(fit)$table[1, ] -- David.> > 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.David Winsemius, MD West Hartford, CT