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simulation_survival_data_simsurv_package.html
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<h1 id="simulation-survival-data">Simulation Survival data</h1>
<p>habib ezatabadi</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(simsurv)) {</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"simsurv"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(simsurv)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(survsim)) {</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"survsim"</span>)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(survsim)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(tidyverse)) {</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"tidyverse"</span>)</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(tidyverse)</span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span>(<span class="sc">!</span> <span class="fu">require</span>(ggsurvfit)) {</span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"ggsurvfit"</span>)</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(ggsurvfit)</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span> (gtsummary)) {</span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"gtsummary"</span>)</span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(gtsummary)</span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span> (tidycmprsk)) {</span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"tidycmprsk"</span>)</span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(tidycmprsk)</span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span> (condSURV)) {</span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"condSURV"</span>)</span>
<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(condSURV)</span>
<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(survival)</span>
<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(survminer)) {</span>
<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"survminer"</span>)</span>
<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(survminer)</span>
<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(magick)) {</span>
<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"magick"</span>)</span>
<span id="cb1-43"><a href="#cb1-43" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(magick)</span>
<span id="cb1-44"><a href="#cb1-44" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-45"><a href="#cb1-45" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-46"><a href="#cb1-46" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(cowplot)) {</span>
<span id="cb1-47"><a href="#cb1-47" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"cowplot"</span>)</span>
<span id="cb1-48"><a href="#cb1-48" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(cowplot)</span>
<span id="cb1-49"><a href="#cb1-49" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-50"><a href="#cb1-50" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-51"><a href="#cb1-51" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-52"><a href="#cb1-52" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(finalfit)) {</span>
<span id="cb1-53"><a href="#cb1-53" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"finalfit"</span>)</span>
<span id="cb1-54"><a href="#cb1-54" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(finalfit)</span>
<span id="cb1-55"><a href="#cb1-55" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-56"><a href="#cb1-56" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-57"><a href="#cb1-57" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(ggpubr)) {</span>
<span id="cb1-58"><a href="#cb1-58" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"ggpubr"</span>)</span>
<span id="cb1-59"><a href="#cb1-59" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(ggpubr)</span>
<span id="cb1-60"><a href="#cb1-60" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-61"><a href="#cb1-61" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-62"><a href="#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(png)) {</span>
<span id="cb1-63"><a href="#cb1-63" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"png"</span>)</span>
<span id="cb1-64"><a href="#cb1-64" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(png)</span>
<span id="cb1-65"><a href="#cb1-65" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb1-66"><a href="#cb1-66" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-67"><a href="#cb1-67" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-68"><a href="#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span> <span class="fu">require</span>(ggimage)) {</span>
<span id="cb1-69"><a href="#cb1-69" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"ggimage"</span>)</span>
<span id="cb1-70"><a href="#cb1-70" aria-hidden="true" tabindex="-1"></a> <span class="fu">library</span>(ggimage)</span>
<span id="cb1-71"><a href="#cb1-71" aria-hidden="true" tabindex="-1"></a>}</span></code></pre></div>
<h2 id="simulate-data">Simulate Data</h2>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="do">## use simsurv package</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">215</span>)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>nsim <span class="ot">=</span> <span class="dv">100</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>Treat <span class="ot"><-</span> <span class="fu">rbinom</span>(<span class="at">n =</span> nsim, <span class="at">size =</span> <span class="dv">1</span>, <span class="at">prob =</span> <span class="fl">0.55</span>)</span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>bp <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="at">n =</span> nsim, <span class="at">mean =</span> <span class="dv">120</span>, <span class="at">sd =</span> <span class="dv">2</span>)</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>dat <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="at">treat =</span> Treat, <span class="at">bp =</span> bp)</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>betas <span class="ot">=</span> <span class="fu">data.frame</span>(<span class="at">lambda =</span> <span class="fu">rep</span>(<span class="dv">4</span>, nsim), <span class="at">beta1 =</span> <span class="fu">rep</span>(<span class="dv">2</span>, nsim), <span class="at">beta2 =</span> <span class="fu">rep</span>(<span class="sc">-</span><span class="dv">3</span>, nsim))</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>hAzard <span class="ot"><-</span> <span class="cf">function</span>(t, x, betas) t <span class="sc">**</span> betas[[<span class="st">'lambda'</span>]] <span class="sc">*</span> <span class="fu">exp</span>(<span class="sc">-</span>betas[<span class="st">'lambda'</span>] <span class="sc">*</span> t <span class="sc">**</span> betas[[<span class="st">'lambda'</span>]] <span class="sc">*</span> (betas[[<span class="st">'beta1'</span>]] <span class="sc">*</span> x[[<span class="st">'treat'</span>]] <span class="sc">+</span> betas[[<span class="st">'beta2'</span>]]<span class="sc">*</span>x[[<span class="st">'bp'</span>]]))</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>Time <span class="ot"><-</span> <span class="fu">simsurv</span>(<span class="at">hazard =</span> hAzard, <span class="at">x =</span> dat, <span class="at">betas =</span> betas, <span class="at">maxt =</span> <span class="dv">2</span>, <span class="at">seed =</span> <span class="dv">215</span>)</span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>Data <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="at">id =</span> Time<span class="sc">$</span>id, <span class="at">Event_time =</span> Time<span class="sc">$</span>eventtime, <span class="at">Status =</span> Time<span class="sc">$</span>status, </span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a> <span class="at">Group =</span> dat<span class="sc">$</span>treat, <span class="at">bp =</span> dat<span class="sc">$</span>bp)</span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a><span class="co"># save(Data, file = "Data.RData")</span></span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a><span class="co"># load("Data.RData")</span></span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a>knitr <span class="sc">::</span> <span class="fu">kable</span>(Data, <span class="at">caption =</span> <span class="st">"Simulated Data"</span>, <span class="at">align =</span> <span class="st">"c"</span>)</span></code></pre></div>
<table>
<thead>
<tr class="header">
<th align="center">id</th>
<th align="center">Event_time</th>
<th align="center">Status</th>
<th align="center">Group</th>
<th align="center">bp</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">0.2831470</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">118.7824</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">0.2870629</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">123.5056</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">0.2915740</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">122.6091</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">0.2720246</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">120.1885</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">0.2661488</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">123.5121</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">0.2787193</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">117.6145</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">0.2666844</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">120.8736</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">0.2762620</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">119.6373</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">0.2908718</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">121.1187</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">0.2917171</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">121.6618</td>
</tr>
<tr class="odd">
<td align="center">11</td>
<td align="center">0.2847885</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">114.5974</td>
</tr>
<tr class="even">
<td align="center">12</td>
<td align="center">0.2831202</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">118.1978</td>
</tr>
<tr class="odd">
<td align="center">13</td>
<td align="center">0.2780252</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">117.2078</td>
</tr>
<tr class="even">
<td align="center">14</td>
<td align="center">0.2836996</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">119.8045</td>
</tr>
<tr class="odd">
<td align="center">15</td>
<td align="center">0.2962747</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">120.1198</td>
</tr>
<tr class="even">
<td align="center">16</td>
<td align="center">0.2847364</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">118.5901</td>
</tr>
<tr class="odd">
<td align="center">17</td>
<td align="center">0.2899293</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">121.2846</td>
</tr>
<tr class="even">
<td align="center">18</td>
<td align="center">0.2923437</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">119.0993</td>
</tr>
<tr class="odd">
<td align="center">19</td>
<td align="center">0.2901060</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">122.2343</td>
</tr>
<tr class="even">
<td align="center">20</td>
<td align="center">0.2925414</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">120.6156</td>
</tr>
<tr class="odd">
<td align="center">21</td>
<td align="center">0.2945615</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">115.4500</td>
</tr>
<tr class="even">
<td align="center">22</td>
<td align="center">0.2870913</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">121.6601</td>
</tr>
<tr class="odd">
<td align="center">23</td>
<td align="center">0.2928195</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">121.1790</td>
</tr>
<tr class="even">
<td align="center">24</td>
<td align="center">0.2769504</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">115.8367</td>
</tr>
<tr class="odd">
<td align="center">25</td>
<td align="center">0.2730274</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">123.0457</td>
</tr>
<tr class="even">
<td align="center">26</td>
<td align="center">0.2783625</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">122.2174</td>
</tr>
<tr class="odd">
<td align="center">27</td>
<td align="center">0.2864162</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">117.4068</td>
</tr>
<tr class="even">
<td align="center">28</td>
<td align="center">0.2723059</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">120.0025</td>
</tr>
<tr class="odd">
<td align="center">29</td>
<td align="center">0.2318162</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">119.0873</td>
</tr>
<tr class="even">
<td align="center">30</td>
<td align="center">0.2850301</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">120.4517</td>
</tr>
<tr class="odd">
<td align="center">31</td>
<td align="center">0.2912149</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">119.0293</td>
</tr>
<tr class="even">
<td align="center">32</td>
<td align="center">0.2889599</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">120.4829</td>
</tr>
<tr class="odd">
<td align="center">33</td>
<td align="center">0.2661675</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">121.4678</td>
</tr>
<tr class="even">
<td align="center">34</td>
<td align="center">0.2907613</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">119.8860</td>
</tr>
<tr class="odd">
<td align="center">35</td>
<td align="center">0.2930568</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">119.0227</td>
</tr>
<tr class="even">
<td align="center">36</td>
<td align="center">0.2829282</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">120.5321</td>
</tr>
<tr class="odd">
<td align="center">37</td>
<td align="center">0.2753554</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">119.0989</td>
</tr>
<tr class="even">
<td align="center">38</td>
<td align="center">0.2851077</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">118.7805</td>
</tr>
<tr class="odd">
<td align="center">39</td>
<td align="center">0.2766302</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">119.1626</td>
</tr>
<tr class="even">
<td align="center">40</td>
<td align="center">0.2886716</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">117.3817</td>
</tr>
<tr class="odd">
<td align="center">41</td>
<td align="center">0.2767017</td>
<td align="center">1</td>
<td align="center">0</td>
<td align="center">122.9102</td>
</tr>
<tr class="even">
<td align="center">42</td>
<td align="center">0.2887925</td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">120.1439</td>
</tr>
<tr class="odd">
<td align="center">43</td>