R help - Jan 2012 - Problem with axes in a plot of Kaplan-Meier

Helo:

After changing "involuntarily" some of the graphics parameters with
the command par() (I did not know that changes with this command are
permanent), now when I made a plot of the survival Kaplan-Meier
function, the Y axis does not start at 1, and the X axis does starts
at 0. The commands that I use are:

    library(survival)
    BROWN.SPV = Surv(BROWN$TEMPS, BROWN$DEF)
    BROWN.KM = survfit(BROWN.SPV ~ 1)
    plot(BROWN.KM$time, BROWN.KM$surv, type="s")

How can I restore previous graphics parameters? Is there a file that
would delete to restore the initial settings (already use R in debian
squeeze)?

Thanks a lot. AGriera

On Jan 5, 2012, at 12:50 PM, correu griera wrote:
> Helo:
>
> After changing "involuntarily" some of the graphics parameters
with
> the command par() (I did not know that changes with this command are
> permanent), now when I made a plot of the survival Kaplan-Meier
> function, the Y axis does not start at 1, and the X axis does starts
> at 0. The commands that I use are:
>
>    library(survival)
>    BROWN.SPV = Surv(BROWN$TEMPS, BROWN$DEF)
>    BROWN.KM = survfit(BROWN.SPV ~ 1)
>    plot(BROWN.KM$time, BROWN.KM$surv, type="s")
I would be happy to be proven wrong, but I don't think so. My idea is  
to add this line to your .Rprofile:

myopar <- par()

Then you can restore in the future with

par(myopar)

(This is untested and at times I fall on my face with initialization  
assumptions. If the graphics package is not loaded at the  
time .Rprofile is interpreted you might need to run require(graphics)  
before that command.)


The usual practice in a console session (if you remember to do this) is:

opar <-par(new-par-specs)
plot-commands
par(opar)

And you should instead be using on.exit if you are writing functions  
to do this.
>
> How can I restore previous graphics parameters? Is there a file that
> would delete to restore the initial settings (already use R in debian
> squeeze)?
>
-- 

David Winsemius, MD
West Hartford, CT

After changing "involuntarily" some of the graphics parameters with
the command par() (I did not know that changes with this command are
permanent), now when I made a plot of the survival Kaplan-Meier
function, the Y axis does not start at 1, and the X axis does starts
at 0. The commands that I use are:

-------------

  Par command are cumulative PER graphics device.  Your "unfortunate"
par commands would not affect a new plot with pdf() for instance.
I often resort to the simple solution of
	dev.off()  #close the current window
	x11() # start a new one
(If not on Unix replace x11 with the appropriate command for your
system).

  David's solution is the more elegant one.

Terry T.