R help - Aug 2008 - Trying to run simple survival program in R but does not work

Hey,

I am just starting to learn R now and I typed in this simple survival
program:
  
   library(survival)
   t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
   c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
   data <- Surv(t,c)
   km <- survfit(data)       
   summary(km)
   Call: survfit(formula = data)

but everytime I run it I get this error:
  
  Error in eval.with.vis(expr, envir, enclos) : object "Call" not
found

Can someone please help me out I really have no idea wat I have done wrong.
I have installed the survival library is there maybe some other library I
need to install?
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When I run your code, I have no problem at all, could you please give us some
more info about what system you are running on, OS, packages loaded, .....

Bart


Trev101 wrote:
> 
> Hey,
> 
> I am just starting to learn R now and I typed in this simple survival
> program:
>   
>    library(survival)
>    t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
>    c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
>    data <- Surv(t,c)
>    km <- survfit(data)       
>    summary(km)
>    Call: survfit(formula = data)
> 
> but everytime I run it I get this error:
>   
>   Error in eval.with.vis(expr, envir, enclos) : object "Call" not
found
> 
> Can someone please help me out I really have no idea wat I have done
> wrong. I have installed the survival library is there maybe some other
> library I need to install?
> 
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Very Strange have no idea why this is happening :-( I am running a AMD Athlon
64 3500+ with 1 GB RAM and Running microsoft Windows XP service pack 2.

I only installed the main program of R being R-2.7.1-win32 and then I
installed tinn-R. I then opened R and tinn-R and then from the RGui I went
to packages, install packages, choose the CRAN mirror in South Africa and
then went down to survival and installed that package. I thought that was
all package I would need to install. Is there something else that I must
install?

Thanx for all the help I really hope to sort this problem out. 
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Oh wait it gives me another error saying that: 
Loading required package: splines

I cant find the package called splines in the list is that an important
package?
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Survival depends on splines, so you should install the splines library, and
then everything should be fine.

Bart


Trevor Hansen wrote:
> 
> Oh wait it gives me another error saying that: 
> Loading required package: splines
> 
> I cant find the package called splines in the list is that an important
> package?
> 
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Hey, Thanx I did that and it works it gives me the output I require but it
still does not like that call option I guess its not that important since I
got the output I required :-D.

Thanx for all the help I really appreciate it :-D
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On Thu, 7 Aug 2008, Trev101 wrote:
>
> Hey,
>
> I am just starting to learn R now and I typed in this simple survival
> program:
>
>   library(survival)
>   t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
>   c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
>   data <- Surv(t,c)
>   km <- survfit(data)
>   summary(km)
>   Call: survfit(formula = data)
>
> but everytime I run it I get this error:
>
>  Error in eval.with.vis(expr, envir, enclos) : object "Call" not
found
>
> Can someone please help me out I really have no idea wat I have done wrong.
You have pasted in part of the output of 'summary(km)': R does not 
understand its own output, only its language.
> I have installed the survival library is there maybe some other library I
> need to install?
> -- 
> View this message in context:
http://www.nabble.com/Trying-to-run-simple-survival-program-in-R-but-does-not-work-tp18865807p18865807.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Trev101 wrote:
> Hey,
>
> I am just starting to learn R now and I typed in this simple survival
> program:
>   
>    library(survival)
>    t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
>    c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
>    data <- Surv(t,c)
>    km <- survfit(data)       
>    summary(km)
>    Call: survfit(formula = data)
>
> but everytime I run it I get this error:
>   
>   Error in eval.with.vis(expr, envir, enclos) : object "Call" not
found
>
> Can someone please help me out I really have no idea wat I have done wrong.
> I have installed the survival library is there maybe some other library I
> need to install
>   
Don't capitalise the "Call" command, use "call" instead.
Good luck!

tomas

p.s.: am I right if I suppose that You are using Windows? ;-)

On 07/08/2008 3:56 AM, Trev101 wrote:
> Hey,
> 
> I am just starting to learn R now and I typed in this simple survival
> program:
>   
>    library(survival)
>    t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
>    c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
>    data <- Surv(t,c)
>    km <- survfit(data)       
>    summary(km)
>    Call: survfit(formula = data)
> 
> but everytime I run it I get this error:
>   
>   Error in eval.with.vis(expr, envir, enclos) : object "Call" not
found
> 
> Can someone please help me out I really have no idea wat I have done wrong.
> I have installed the survival library is there maybe some other library I
> need to install?
The last line, "Call: survfit(formula = data)", is not R code.  It is 
the first line of the output you should expect to see, i.e.

 >  library(survival)
Loading required package: splines
 >    t <- c(10,13,18,19,23,30,36,38,54,56,59,75,93,97,104,107,107,107)
 >    c <- c(1,0,0,1,0,1,1,0,0,0,1,1,1,1,0,1,0,0)
 >    data <- Surv(t,c)
 >    km <- survfit(data)
 >    summary(km)
Call: survfit(formula = data)

  time n.risk n.event survival std.err lower 95% CI upper 95% CI
    10     18       1    0.944  0.0540        0.844        1.000
    19     15       1    0.881  0.0790        0.739        1.000
    30     13       1    0.814  0.0978        0.643        1.000
    36     12       1    0.746  0.1107        0.558        0.998
    59      8       1    0.653  0.1303        0.441        0.965
    75      7       1    0.559  0.1412        0.341        0.917
    93      6       1    0.466  0.1452        0.253        0.858
    97      5       1    0.373  0.1430        0.176        0.791
   107      3       1    0.249  0.1392        0.083        0.745

Duncan Murdoch