[R] grouping scat1d/rug and plotting to 2 axes
Frank E Harrell Jr
f.harrell at vanderbilt.edu
Mon Aug 27 23:27:30 CEST 2007
> I'm wondering if anybody can offer a bit of guidance on how to add a
> couple of features to a plot.
> I'm using Frank Harrell's Design library to model some survival data in
> R (2.3.1, windows platform). I'm fairly comfortable with the survival
> modeling in Design, but am still at a frustratingly low level of
> competence when it comes to creating anything beyond simple plots in R.
> A simplified version of the model is:
> fit <- cph(Surv(survtime,deceased) ~ rcs(smw,4),
> data=survdata,x=T,y=T,surv=T )
> And the basic plot is:
> plot(fit,smw=NA, fun=function(x) 1/(1+exp(-x)))
or plot(fit, smw=NA, fun=plogis). But what does the logistic model have
to do with the Cox model you fitted? You can instead do plot(fit,
smw=NA, time=1) to plot estimated 1-year survival prob.
> I know that if I add
> I get a nice jittered rug plot of all values of the predictor smw on the
> top axis.
> What I'd like to do, however, is to plot on bottom axis the values of
> smw for only those participants who are alive, and then on the top axis,
> plot the values of smw for those who are deceased. I'd appreciate any
> tips as to how I might approach this.
That isn't so well defined because of variable follow-up time. I would
not get very much out of such a plot.
> Mike Babyak
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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