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raymond chiruka

2007-Oct-29 09:04 UTC

[R] using survfit

hie 
  when i use plot.survfit to plot more than one graph why I only see the last
graph how do i see the other graphs.for example
  
      n=20
      n1=n/2
      n2=n/4
      a11=4;a12=4 ;a21=4 ;a22=4
      t1<-array(1,c(n1))                                             
       t2<-array(2,c(n1))
      treatgrp=matrix(c(t1,t2))                                    
      st11<-array(1,c(n2))
       st12<-array(2,c(n2))
       st21<-array(1,c(n2))
       st22<-array(2,c(n2))
      strata=matrix(c(st11,st12,st21,st22))                 
      time11=array(rweibull(n2,a11,1))
      time12=array(rweibull(n2,a11,1))
      time21=array(rweibull(n2,a21,1))
      time22=array(rweibull(n2,a22,1))
      time=matrix(c(time11, time12, time21, time22))  
      censorTime=runif(n,0,3)
      m=cbind(treatgrp,strata,time,censorTime)                 
      colnames(m)=c(“treat”,”strata”,”time”,”censorTime”)
      
act.surv.time<-pmin(m[,"time"],m[,"censorTime"])
  
m<-cbind(m,act.surv.time)
      m<-cbind(m,0)
         m[m[,3]<m[,4],6]<-1
         colnames(m)[6]<-"censoring"
      m
      b=data.frame(m)
      
d2=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,type=c("fleming-harrington"),
  
)
  
plot(d2, lty=2:3, fun="cumhaz",
  
        xlab="Months", ylab="Cumulative Hazard")
  
d1=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,)
  
plot(d1, lty=2:3,
  
        xlab="Months", ylab="survival curves")

I only see the plot of d1 what happens to d2 and how do l view it.
thanks


  
  
 __________________________________________________



	[[alternative HTML version deleted]]

Ritwik Sinha

2007-Oct-29 14:39 UTC

head link

[R] using survfit

Hi,

You can use the par function to set the parameters of the plot to have
multiple plots in one output. Have something like par(mfrow=c(2,1)) before
your plot commands.

You could also write the the outputs to a ps, pdf or jpeg file (look for the
pdf, postscript and jpeg commands). That way the plots would not be
overwritten.

Ritwik


On 10/29/07, raymond chiruka <rtchiruka@yahoo.com>
wrote:>
> hie
>   when i use plot.survfit to plot more than one graph why I only see the
> last graph how do i see the other graphs.for example
>
>       n=20
>       n1=n/2
>       n2=n/4
>       a11=4;a12=4 ;a21=4 ;a22=4
>       t1<-array(1,c(n1))
>        t2<-array(2,c(n1))
>       treatgrp=matrix(c(t1,t2))
>       st11<-array(1,c(n2))
>        st12<-array(2,c(n2))
>        st21<-array(1,c(n2))
>        st22<-array(2,c(n2))
>       strata=matrix(c(st11,st12,st21,st22))
>       time11=array(rweibull(n2,a11,1))
>       time12=array(rweibull(n2,a11,1))
>       time21=array(rweibull(n2,a21,1))
>       time22=array(rweibull(n2,a22,1))
>       time=matrix(c(time11, time12, time21, time22))
>       censorTime=runif(n,0,3)
>       m=cbind(treatgrp,strata,time,censorTime)
>      
colnames(m)=c("treat","strata","time","censorTime")
>
> act.surv.time<-pmin(m[,"time"],m[,"censorTime"])
>
> m<-cbind(m,act.surv.time)
>       m<-cbind(m,0)
>          m[m[,3]<m[,4],6]<-1
>          colnames(m)[6]<-"censoring"
>       m
>       b=data.frame(m)
>
> d2=survfit(Surv(act.surv.time
> ,censoring)~treatgrp,data=b,type=c("fleming-harrington"),
>
> )
>
> plot(d2, lty=2:3, fun="cumhaz",
>
>         xlab="Months", ylab="Cumulative Hazard")
>
> d1=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,)
>
> plot(d1, lty=2:3,
>
>         xlab="Months", ylab="survival curves")
>
> I only see the plot of d1 what happens to d2 and how do l view it.
> thanks
>
>
>
>
> __________________________________________________
>
>
>
>         [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help@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.
>
>

-- 
Ritwik Sinha
ritwik.sinha@gmail.com | +12033042111 | http://darwin.cwru.edu/~rsinha

	[[alternative HTML version deleted]]

David Winsemius

2007-Oct-30 00:14 UTC

head link

[R] using survfit

raymond chiruka wrote:> hie 
>   when i use plot.survfit to plot more than one graph why I only see the
last graph how do i see the other graphs.for example
>   
>       n=20
>       n1=n/2
>       n2=n/4
>       a11=4;a12=4 ;a21=4 ;a22=4
>       t1<-array(1,c(n1))                                             
>        t2<-array(2,c(n1))
>       treatgrp=matrix(c(t1,t2))                                    
>       st11<-array(1,c(n2))
>        st12<-array(2,c(n2))
>        st21<-array(1,c(n2))
>        st22<-array(2,c(n2))
>       strata=matrix(c(st11,st12,st21,st22))                 
>       time11=array(rweibull(n2,a11,1))
>       time12=array(rweibull(n2,a11,1))
>       time21=array(rweibull(n2,a21,1))
>       time22=array(rweibull(n2,a22,1))
>       time=matrix(c(time11, time12, time21, time22))  
>       censorTime=runif(n,0,3)
>       m=cbind(treatgrp,strata,time,censorTime)                 
>       colnames(m)=c(?treat?,?strata?,?time?,?censorTime?)
>   
My version of R (2.4.1 on a WindozeXP machine) had problems with the 
"smart-quotes" when cut and pasted but I cannot be sure that was not a
problem induced by Thunderbird.
>       
> act.surv.time<-pmin(m[,"time"],m[,"censorTime"])
>   
> m<-cbind(m,act.surv.time)
>       m<-cbind(m,0)
>          m[m[,3]<m[,4],6]<-1
>          colnames(m)[6]<-"censoring"
>       m
>       b=data.frame(m)
>       
>
d2=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,type=c("fleming-harrington"),
>   
> )
>   
> plot(d2, lty=2:3, fun="cumhaz",
>   
>         xlab="Months", ylab="Cumulative Hazard")
>   
It plotted just fine. And you then over-wrote it with the second plot. 
You could save (temporarily) a screen plot with
 > surv.crv<-recordPlot()
### then make another plot, save it too.
### then use
 > replayPlot(surv.crv)

You could also save to a file and view in an external viewer. The format 
of recorded plots is not guaranteed to be the same from version to version.

Another option (which would be machine specific and assuming a Windows 
device) would be to open second screen window with:

 > win.graph(width = 7, height = 7, pointsize = 12, restoreConsole = FALSE)
>   
> d1=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,)
>   
> plot(d1, lty=2:3,
>   
>         xlab="Months", ylab="survival curves")
>
> I only see the plot of d1 what happens to d2 and how do l view it.
> thanks
>   
If you opened a new device before each plot you could paper your screen 
with plots.

-- 
David Winsemius

Daniel Malter

2007-Oct-30 02:09 UTC

head link

[R] using survfit

Hi, you may look here http://www.ats.ucla.edu/stat/examples/asa/ to find an
answer to your question. Basically you have to overlay one graph with the
points (lines) that you want to add. Otherwise, R replaces the old graph by
the new and does not add it as far as I know.

Cheers,
Daniel


-------------------------
cuncta stricte discussurus
-------------------------

-----Urspr?ngliche Nachricht-----
Von: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Im
Auftrag von David Winsemius
Gesendet: Monday, October 29, 2007 8:15 PM
An: r
Betreff: Re: [R] using survfit

raymond chiruka wrote:> hie 
>   when i use plot.survfit to plot more than one graph why I only see 
> the last graph how do i see the other graphs.for example
>   
>       n=20
>       n1=n/2
>       n2=n/4
>       a11=4;a12=4 ;a21=4 ;a22=4
>       t1<-array(1,c(n1))                                             
>        t2<-array(2,c(n1))
>       treatgrp=matrix(c(t1,t2))                                    
>       st11<-array(1,c(n2))
>        st12<-array(2,c(n2))
>        st21<-array(1,c(n2))
>        st22<-array(2,c(n2))
>       strata=matrix(c(st11,st12,st21,st22))                 
>       time11=array(rweibull(n2,a11,1))
>       time12=array(rweibull(n2,a11,1))
>       time21=array(rweibull(n2,a21,1))
>       time22=array(rweibull(n2,a22,1))
>       time=matrix(c(time11, time12, time21, time22))  
>       censorTime=runif(n,0,3)
>       m=cbind(treatgrp,strata,time,censorTime)                 
>       colnames(m)=c(?treat?,?strata?,?time?,?censorTime?)
>   
My version of R (2.4.1 on a WindozeXP machine) had problems with the
"smart-quotes" when cut and pasted but I cannot be sure that was not a
problem induced by Thunderbird.
>       
> act.surv.time<-pmin(m[,"time"],m[,"censorTime"])
>   
> m<-cbind(m,act.surv.time)
>       m<-cbind(m,0)
>          m[m[,3]<m[,4],6]<-1
>          colnames(m)[6]<-"censoring"
>       m
>       b=data.frame(m)
>       
> d2=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,type=c("flemi
> ng-harrington"),
>   
> )
>   
> plot(d2, lty=2:3, fun="cumhaz",
>   
>         xlab="Months", ylab="Cumulative Hazard")
>   
It plotted just fine. And you then over-wrote it with the second plot. 
You could save (temporarily) a screen plot with  > surv.crv<-recordPlot()
### then make another plot, save it too.
### then use
 > replayPlot(surv.crv)

You could also save to a file and view in an external viewer. The format of
recorded plots is not guaranteed to be the same from version to version.

Another option (which would be machine specific and assuming a Windows
device) would be to open second screen window with:

 > win.graph(width = 7, height = 7, pointsize = 12, restoreConsole = FALSE)
>   
> d1=survfit(Surv(act.surv.time,censoring)~treatgrp,data=b,)
>   
> plot(d1, lty=2:3,
>   
>         xlab="Months", ylab="survival curves")
>
> I only see the plot of d1 what happens to d2 and how do l view it.
> thanks
>   
If you opened a new device before each plot you could paper your screen with
plots.

--
David Winsemius

______________________________________________
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.

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