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POGenerating/plotting a log-normal survival function
 

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  1. POGenerating/plotting a log-normal survival function
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    <p>I have an accelerated failure time model in SAS LIFEREG that I'd like to plot. Because SAS is to profoundly bad at graphing, I'd like to actually re-generate the data for the curves in R and plot them there. SAS puts out a scale (in the case of the exponential distribution fixed to 1), an intercept, and a regression coefficient for being in the exposed or unexposed population.</p> <p>There's two curves, one for the exposed and one for the unexposed population. One of the models is an exponential distribution, and I've produced the data and graph like so:</p> <pre><code>intercept &lt;- 5.00 effect&lt;- -0.500 data&lt;- data.frame(time=seq(0:180)-1) data$s_unexposed &lt;- apply(data,1,function(row) exp(-(exp(-intercept))*row[1])) data$s_exposed &lt;- apply(data,1,function(row) exp(-(exp(-(intercept+effect))*row[1]))) plot(data$time,data$s_unexposed, type="l", ylim=c(0,1) ,xaxt='n', xlab="Days since Infection", ylab="Percent Surviving", lwd=2) axis(1, at=c(0, 20, 40, 60, 80, 100, 120, 140, 160, 180)) lines(data$time,data$s_exposed, col="red",lwd=2) legend("topright", c("ICU Patients", "Non-ICU Patients"), lwd=2, col=c("red","black") ) </code></pre> <p>Which gives me this:</p> <p><img src="https://i.stack.imgur.com/IDgHg.png" alt="enter image description here"></p> <p>Not the prettiest graph ever, but I don't really know my way around ggplot2 enough to spruce it up. But more importantly, I have a second set of data that comes from a Log Normal distribution, rather than an exponential, and my attempts to generate the data for that have failed utterly - the incorporation of the cdf for the normal distribution and the like puts it beyond my R skills. </p> <p>Anyone able to point me in the right direction, using the same numbers, and a scale parameter of 1?</p>
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    1. COWhen you use ODS SAS generally provides very nice curves now. Without using SAS Graph isn't there an option in SAS to plot survival curves? It could be that there is a default graph that would look good.
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      1. USMichael Chernick
    2. COIn my opinion, this question is within the SO-CV overlap, but a closer fit for CV than SO. It is a programming question, but it needs some *statistical expertise* to answer, and thus belongs on CV as per CV's [faq](http://stats.stackexchange.com/faq).
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    3. CO@MichaelChernick As far as I can tell, LIFEREG can produce a *hazard* plot and some diagnostic plots, but not a survival function. To be fair, most people are looking to LIFETEST to produce survival functions normally - but I'm not in this particular case.
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