https://github.com/cran/rstpm2
Tip revision: c12a9847539968aa375d4df8349a3a524e7c1bb5 authored by Mark Clements on 17 January 2019, 14:50:04 UTC
version 1.4.5
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Tip revision: c12a984
timevar.html
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<div id="content">
<h1 class="title">Predictions</h1>
<div id="outline-container-orgheadline1" class="outline-2">
<h2 id="orgheadline1"><span class="section-number-2">1</span> R implementation for <a href="https://pclambert.net/software/stpm2/stpm2_timevar/">https://pclambert.net/software/stpm2/stpm2_timevar/</a></h2>
<div class="outline-text-2" id="text-1">
<div class="org-src-container">
<pre class="src src-R"><span style="color: #008b8b;">library</span>(rstpm2)
<span style="color: #008b8b;">library</span>(readstata13)
suppressWarnings(rott2b <span style="color: #008b8b;"><-</span> read.dta13(<span style="color: #8b2252;">"https://www.pclambert.net/data/rott2b.dta"</span>))
rott2b <span style="color: #008b8b;"><-</span> transform(rott2b, time = pmin(rf,60)/12)
rott2b <span style="color: #008b8b;"><-</span> transform(rott2b, event = (rfi==1) & (time < 60/12))
fit <span style="color: #008b8b;"><-</span> stpm2(Surv(time,event) ~ hormon + nsx(age,df=3,centre=60,stata=<span style="color: #228b22;">TRUE</span>) + pr_1,
data=rott2b, df=4, stata=<span style="color: #228b22;">TRUE</span>)
eform(fit)
</pre>
</div>
<pre class="example">
Profiling...
exp(beta) 2.5 % 97.5 %
(Intercept) 6.055607e-04 5.715701e-04 6.402896e-04
hormonyes 1.253597e+00 1.065865e+00 1.462097e+00
nsx(age, df = 3, centre = 60, stata = TRUE)1 6.550003e-01 5.594371e-01 7.702334e-01
nsx(age, df = 3, centre = 60, stata = TRUE)2 3.449221e-01 1.993938e-01 5.962187e-01
nsx(age, df = 3, centre = 60, stata = TRUE)3 9.626652e-01 7.189637e-01 1.275743e+00
pr_1 9.080228e-01 8.944134e-01 9.214805e-01
nsx(log(time), df = 4)1 4.474345e+02 4.148646e+02 4.799754e+02
nsx(log(time), df = 4)2 1.974220e+02 1.894423e+02 2.047062e+02
nsx(log(time), df = 4)3 5.391834e+04 4.862060e+04 5.986957e+04
nsx(log(time), df = 4)4 7.282589e+01 6.949526e+01 7.650186e+01
</pre>
<div class="org-src-container">
<pre class="src src-R">nd <span style="color: #008b8b;"><-</span> data.frame(age=60, hormon=<span style="color: #8b2252;">"no"</span>, pr_1=0)
plot(fit, type=<span style="color: #8b2252;">"surv"</span>, newdata=nd, xlab=<span style="color: #8b2252;">"Years from surgery"</span>)
</pre>
</div>
<div class="figure">
<p><img src="surv_1.png" alt="surv_1.png" />
</p>
</div>
<div class="org-src-container">
<pre class="src src-R"><span style="color: #008b8b;">library</span>(ggplot2)
nd <span style="color: #008b8b;"><-</span> data.frame(age=60, hormon=c(<span style="color: #8b2252;">"no"</span>,<span style="color: #8b2252;">"yes"</span>), pr_1=0)
haz <span style="color: #008b8b;"><-</span> predict(fit, type=<span style="color: #8b2252;">"haz"</span>, newdata=nd, grid=<span style="color: #228b22;">TRUE</span>, se.fit=<span style="color: #228b22;">TRUE</span>, keep=<span style="color: #228b22;">TRUE</span>)
haz <span style="color: #008b8b;"><-</span> cbind(haz,attr(haz,<span style="color: #8b2252;">"newdata"</span>))
ggplot(haz, aes(time,group=hormon)) + geom_line(aes(y=Estimate,colour=hormon)) + geom_ribbon(aes(ymin=lower,ymax=upper), alpha=0.2) + xlab(<span style="color: #8b2252;">"Time since surgery (years)"</span>) + ylab(<span style="color: #8b2252;">"Hazard"</span>)
</pre>
</div>
<div class="figure">
<p><img src="haz_1.png" alt="haz_1.png" />
</p>
</div>
<div class="org-src-container">
<pre class="src src-R">s_time1 <span style="color: #008b8b;"><-</span> predict(fit, newdata=transform(rott2b, time=1), type=<span style="color: #8b2252;">"surv"</span>)
hist(s_time1,xlab=<span style="color: #8b2252;">"Time from surgery"</span>,main=<span style="color: #8b2252;">""</span>)
</pre>
</div>
<div class="figure">
<p><img src="histo_1.png" alt="histo_1.png" />
</p>
</div>
<div class="org-src-container">
<pre class="src src-R">s_time5 <span style="color: #008b8b;"><-</span> predict(fit, newdata=transform(rott2b, time=5), type=<span style="color: #8b2252;">"surv"</span>)
hist(s_time5,xlab=<span style="color: #8b2252;">"Time from surgery"</span>,main=<span style="color: #8b2252;">""</span>)
</pre>
</div>
<div class="figure">
<p><img src="histo_2.png" alt="histo_2.png" />
</p>
</div>
<div class="org-src-container">
<pre class="src src-R"><span style="color: #008b8b;">library</span>(ggplot2)
nd <span style="color: #008b8b;"><-</span> with(rott2b, data.frame(age=seq(min(age), max(age), length=301), hormon=<span style="color: #8b2252;">"no"</span>, pr_1=3.43, time=1))
s <span style="color: #008b8b;"><-</span> cbind(nd,predict(fit, newdata=nd, type=<span style="color: #8b2252;">"surv"</span>, se.fit=<span style="color: #228b22;">TRUE</span>))
ggplot(s,aes(age)) + geom_line(aes(y=Estimate)) + geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.2) +
xlab(<span style="color: #8b2252;">"Age (years)"</span>) + ylab(<span style="color: #8b2252;">"Survival"</span>)
</pre>
</div>
<div class="figure">
<p><img src="surv_1_age.png" alt="surv_1_age.png" />
</p>
</div>
<div class="org-src-container">
<pre class="src src-R">s <span style="color: #008b8b;"><-</span> cbind(nd,predict(fit, newdata=transform(nd,time=5), type=<span style="color: #8b2252;">"surv"</span>, se.fit=<span style="color: #228b22;">TRUE</span>))
ggplot(s,aes(age)) + geom_line(aes(y=Estimate)) + geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.2) +
xlab(<span style="color: #8b2252;">"Age (years)"</span>) + ylab(<span style="color: #8b2252;">"Survival"</span>)
</pre>
</div>
<div class="figure">
<p><img src="surv_5_age.png" alt="surv_5_age.png" />
</p>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Mark Clements</p>
<p class="date">Created: 2018-08-03 Fri 10:35</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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