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- <h1 id="seo-header">比较两个COXPH模型的性能</h1>
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- <h2 id="安装补充包"><a href="#安装补充包" class="headerlink" title="安装补充包"></a>安装补充包</h2><ul>
- <li><p><a target="_blank" rel="noopener" href="https://occdn.limour.top/2213.html">conda activate ggsurvplot</a></p>
- </li>
- <li><p>install.packages(‘survIDINRI’)</p>
- </li>
- </ul>
- <h2 id="构建两个COXPH模型"><a href="#构建两个COXPH模型" class="headerlink" title="构建两个COXPH模型"></a>构建两个COXPH模型</h2><h3 id="准备数据"><a href="#准备数据" class="headerlink" title="准备数据"></a>准备数据</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>car<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>rms<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>pROC<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>timeROC<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggDCA<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survivalROC<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>pec<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggsci<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span><span class="hljs-string">"scales"</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>nomogramFormula<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survIDINRI<span class="hljs-punctuation">)</span><br>df1 <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'df.rds'</span><span class="hljs-punctuation">)</span><br>df2 <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'clinical.rds'</span><span class="hljs-punctuation">)</span><br>df <span class="hljs-operator"><-</span> cbind<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>df2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">11</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>df2<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="选择配色"><a href="#选择配色" class="headerlink" title="选择配色"></a>选择配色</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs R">pal_nejm<span class="hljs-punctuation">(</span><span class="hljs-string">"default"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">(</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>show_col<span class="hljs-punctuation">(</span>pal_nejm<span class="hljs-punctuation">(</span><span class="hljs-string">"default"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">(</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#挑选配色</span><br></code></pre></td></tr></table></figure>
- <h3 id="计算某风险指标"><a href="#计算某风险指标" class="headerlink" title="计算某风险指标"></a>计算某风险指标</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br></pre></td><td class="code"><pre><code class="hljs R">coxmf1 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">"Surv(time, status==1)~"</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">11</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">'+'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>coxmf1<br>f1 <span class="hljs-operator"><-</span> cph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data<span class="hljs-operator">=</span>df1<span class="hljs-punctuation">,</span> x<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> surv <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建COX比例风险模型</span><br>surv1 <span class="hljs-operator"><-</span> Survival<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建生存概率函数</span><br>dd<span class="hljs-operator">=</span>datadist<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>datadist<span class="hljs-operator">=</span><span class="hljs-string">"dd"</span><span class="hljs-punctuation">)</span> <br>nom1 <span class="hljs-operator"><-</span> nomogram<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span> fun<span class="hljs-operator">=</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv1<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv1<span class="hljs-punctuation">(</span><span class="hljs-number">3</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv1<span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> funlabel<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"1-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"3-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"5-year Disease-free Probability"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>nom1<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><br>results <span class="hljs-operator"><-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom1<span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>f1_points <span class="hljs-operator"><-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>df<span class="hljs-punctuation">)</span><br>df<br>years1 <span class="hljs-operator"><-</span> timeROC<span class="hljs-punctuation">(</span><span class="hljs-built_in">T</span><span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span>delta<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><br> marker<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>f1_points<span class="hljs-punctuation">,</span>cause<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br> weighting<span class="hljs-operator">=</span><span class="hljs-string">"marginal"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-comment"># other_markers=as.matrix(df$`1-year`),</span><br> times<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ROC<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> iid<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>years1<br>auc1.ci <span class="hljs-operator"><-</span> confint<span class="hljs-punctuation">(</span>years1<span class="hljs-punctuation">,</span> parm<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> level <span class="hljs-operator">=</span> <span class="hljs-number">0.95</span><span class="hljs-punctuation">,</span>n.sim<span class="hljs-operator">=</span><span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>auc1.ci <span class="hljs-operator"><-</span> auc1.ci<span class="hljs-operator">$</span>CI_AUC<br>auc1.ci<br>years1.auc1 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years1<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years1.auc2 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years1<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years1.auc3 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years1<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc1.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>years1<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>title<span class="hljs-operator">=</span><span class="hljs-string">"Time dependent ROC"</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years1<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years1<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">"bottomright"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 1-year ="</span><span class="hljs-punctuation">,</span>years1.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 3-year ="</span><span class="hljs-punctuation">,</span>years1.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 5-year ="</span><span class="hljs-punctuation">,</span>years1.auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="计算第一个模型"><a href="#计算第一个模型" class="headerlink" title="计算第一个模型"></a>计算第一个模型</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br></pre></td><td class="code"><pre><code class="hljs R">dd<span class="hljs-operator">=</span>datadist<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>datadist<span class="hljs-operator">=</span><span class="hljs-string">"dd"</span><span class="hljs-punctuation">)</span> <br>coxmf2 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">"Surv(time, status==1)~PSA+Age+T2vs3+N0vs1+GS"</span><span class="hljs-punctuation">)</span><br>coxmf2<br>f2 <span class="hljs-operator"><-</span> cph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data<span class="hljs-operator">=</span>df<span class="hljs-punctuation">,</span> x<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> surv <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建COX比例风险模型</span><br>surv2 <span class="hljs-operator"><-</span> Survival<span class="hljs-punctuation">(</span>f2<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建生存概率函数</span><br>nom2 <span class="hljs-operator"><-</span> nomogram<span class="hljs-punctuation">(</span>f2<span class="hljs-punctuation">,</span> fun<span class="hljs-operator">=</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv2<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv2<span class="hljs-punctuation">(</span><span class="hljs-number">3</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv2<span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> funlabel<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"1-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"3-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"5-year Disease-free Probability"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>nom2<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><br>results <span class="hljs-operator"><-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom2<span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>f2_points <span class="hljs-operator"><-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>df<span class="hljs-punctuation">)</span><br>df<br>years2 <span class="hljs-operator"><-</span> timeROC<span class="hljs-punctuation">(</span><span class="hljs-built_in">T</span><span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span>delta<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><br> marker<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>f2_points<span class="hljs-punctuation">,</span>cause<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br> weighting<span class="hljs-operator">=</span><span class="hljs-string">"marginal"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-comment"># other_markers=as.matrix(df$`1-year`),</span><br> times<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ROC<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> iid<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>years2<br>auc2.ci <span class="hljs-operator"><-</span> confint<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span> parm<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> level <span class="hljs-operator">=</span> <span class="hljs-number">0.95</span><span class="hljs-punctuation">,</span>n.sim<span class="hljs-operator">=</span><span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>auc2.ci <span class="hljs-operator"><-</span> auc2.ci<span class="hljs-operator">$</span>CI_AUC<br>auc2.ci<br>years2.auc1 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years2.auc2 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years2.auc3 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>title<span class="hljs-operator">=</span><span class="hljs-string">"Time dependent ROC"</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">"bottomright"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 1-year ="</span><span class="hljs-punctuation">,</span>years2.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 3-year ="</span><span class="hljs-punctuation">,</span>years2.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 5-year ="</span><span class="hljs-punctuation">,</span>years2.auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="计算第二个模型"><a href="#计算第二个模型" class="headerlink" title="计算第二个模型"></a>计算第二个模型</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br></pre></td><td class="code"><pre><code class="hljs R">coxmf3 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">"Surv(time, status==1)~PSA+Age+T2vs3+N0vs1+GS+f1_points"</span><span class="hljs-punctuation">)</span><br>coxmf3<br>res.cox <span class="hljs-operator"><-</span> coxph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> df<span class="hljs-punctuation">)</span><br>tmp_res <span class="hljs-operator"><-</span> summary<span class="hljs-punctuation">(</span>res.cox<span class="hljs-punctuation">)</span><br>tmp_res<br>f3 <span class="hljs-operator"><-</span> cph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data<span class="hljs-operator">=</span>df<span class="hljs-punctuation">,</span> x<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> surv <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建COX比例风险模型</span><br>surv3 <span class="hljs-operator"><-</span> Survival<span class="hljs-punctuation">(</span>f3<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建生存概率函数</span><br>nom3 <span class="hljs-operator"><-</span> nomogram<span class="hljs-punctuation">(</span>f3<span class="hljs-punctuation">,</span> fun<span class="hljs-operator">=</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv3<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv3<span class="hljs-punctuation">(</span><span class="hljs-number">3</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">,</span><br> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>surv3<span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> funlabel<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"1-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"3-year Disease-free Probability"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-string">"5-year Disease-free Probability"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>nom3<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><br>results <span class="hljs-operator"><-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom3<span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>f3_points <span class="hljs-operator"><-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>df<span class="hljs-punctuation">)</span><br>df<br>years3 <span class="hljs-operator"><-</span> timeROC<span class="hljs-punctuation">(</span><span class="hljs-built_in">T</span><span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span>delta<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><br> marker<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>f3_points<span class="hljs-punctuation">,</span>cause<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br> weighting<span class="hljs-operator">=</span><span class="hljs-string">"marginal"</span><span class="hljs-punctuation">,</span><br> <span class="hljs-comment"># other_markers=as.matrix(df$`1-year`),</span><br> times<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ROC<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> iid<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>years3<br>auc3.ci <span class="hljs-operator"><-</span> confint<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span> parm<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> level <span class="hljs-operator">=</span> <span class="hljs-number">0.95</span><span class="hljs-punctuation">,</span>n.sim<span class="hljs-operator">=</span><span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>auc3.ci <span class="hljs-operator"><-</span> auc3.ci<span class="hljs-operator">$</span>CI_AUC<br>auc3.ci<br>years3.auc1 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years3<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years3.auc2 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years3<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>years3.auc3 <span class="hljs-operator"><-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years3<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">'('</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">'~'</span><span class="hljs-punctuation">,</span>auc3.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">')%'</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>title<span class="hljs-operator">=</span><span class="hljs-string">"Time dependent ROC"</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">"bottomright"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 1-year ="</span><span class="hljs-punctuation">,</span>years3.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 3-year ="</span><span class="hljs-punctuation">,</span>years3.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"AUC of 5-year ="</span><span class="hljs-punctuation">,</span>years3.auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="比较ROC曲线"><a href="#比较ROC曲线" class="headerlink" title="比较ROC曲线"></a>比较ROC曲线</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs R">options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>title<span class="hljs-operator">=</span><span class="hljs-string">"Time dependent ROC"</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#20854EFF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#7876B1FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#6F99ADFF"</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years3<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">"bottomright"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">"Old AUC of 1-year ="</span><span class="hljs-punctuation">,</span>years2.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"New AUC of 1-year ="</span><span class="hljs-punctuation">,</span>years3.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"Old AUC of 3-year ="</span><span class="hljs-punctuation">,</span>years2.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"New AUC of 3-year ="</span><span class="hljs-punctuation">,</span>years3.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"Old AUC of 5-year ="</span><span class="hljs-punctuation">,</span>years2.auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> paste<span class="hljs-punctuation">(</span><span class="hljs-string">"New AUC of 5-year ="</span><span class="hljs-punctuation">,</span>years3.auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#20854EFF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#BC3C29FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#7876B1FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#0072B5FF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#6F99ADFF"</span><span class="hljs-punctuation">,</span><span class="hljs-string">"#E18727FF"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br>compare<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span>years3<span class="hljs-punctuation">,</span>adjusted<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="计算NRI和IDI"><a href="#计算NRI和IDI" class="headerlink" title="计算NRI和IDI"></a>计算NRI和IDI</h2><ul>
- <li>NRI = (c1-b1)/N1 + (b2-c2)/N2</li>
- <li>a1表示在患病组中新模型和旧模型都分类正确的样本数，b1则表示旧模型分类正确而新模型分类错误，b1越小越好，c1反映了从旧模型到新模型预测的改善情况，c1越大表示改进越多，同理计算出非患病组的a2、b2、c2、d2数值。</li>
- <li>当NRI>0,则为正改善，表示新模型较旧模型对事件的预测能力更好；</li>
- <li>IDI = (Pnew,events - Pold,events) - (Pnew,non-events - Pold,non-events)</li>
- <li>其中Pnew,events、Pold,events表示在患者组中，新模型和旧模型对于每个个体预测疾病发生概率的平均值，两者相减表示预测概率提高的变化量，对于患者来说，预测患病的概率越高，模型越准确，因此差值越大则提示新模型越好。</li>
- <li>而Pnew,non-events、Pold,non-events表示在非患者组中，新模型和旧模型对于每个个体预测疾病发生概率的平均值，两者相减表示预测概率减少的量，对于非患者来说，预测患病的概率越低，模型越准确，因此差值越小则提示新模型越好。</li>
- <li>与NRI类似，若IDI>0，则为正改善，说明新模型比旧模型的预测能力有所改善；</li>
- </ul>
- <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs R">covs0 <span class="hljs-operator"><-</span> as.matrix<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'PSA'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Age'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'T2vs3'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'N0vs1'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'GS'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>covs1 <span class="hljs-operator"><-</span> as.matrix<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'PSA'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Age'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'T2vs3'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'N0vs1'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'GS'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'f1_points'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>t1<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><br>res.IDI <span class="hljs-operator"><-</span> IDI.INF<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'time'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'status'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> covs0<span class="hljs-punctuation">,</span> covs1<span class="hljs-punctuation">,</span> t1<span class="hljs-punctuation">,</span> npert<span class="hljs-operator">=</span><span class="hljs-number">1000</span><span class="hljs-punctuation">)</span><br>IDI.INF.OUT<span class="hljs-punctuation">(</span>res.IDI<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># M1表示IDI</span><br><span class="hljs-comment"># M2表示NRI</span><br><span class="hljs-comment"># M3表示中位数差异</span><br>IDI.INF.GRAPH<span class="hljs-punctuation">(</span>res.IDI<span class="hljs-punctuation">)</span><br><span class="hljs-comment">## M1 red area; M2 distance between black points; M3 distance between gray points</span><br></code></pre></td></tr></table></figure>
- <h2 id="绘制临床决策曲线DCA"><a href="#绘制临床决策曲线DCA" class="headerlink" title="绘制临床决策曲线DCA"></a>绘制临床决策曲线DCA</h2><ul>
- <li>DCA曲线，即决策曲线分析法（Decision Curve Analysis）,是用来帮助确定高风险患者进行干预，而低风险患者避免干预（避免过度医疗），即评价患者获益程度的一种评估方法。</li>
- <li>图中有两条虚线，横着的那条虚线表示所有样本均不进行干预，净获益为0，斜的虚线表示所有样本均进行干预。</li>
- <li>与两条虚线有交叉的模型没有临床价值，在上面的曲线临床价值比在下面的曲线大</li>
- </ul>
- <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">dca_p <span class="hljs-operator"><-</span> dca<span class="hljs-punctuation">(</span>f2<span class="hljs-punctuation">,</span> f3<span class="hljs-punctuation">,</span> times<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> <span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br>ggplot<span class="hljs-punctuation">(</span>dca_p<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> scale_color_nejm<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
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- res.push('.markdown-body > ' + item.trim());
- }
- if (CONFIG.anchorjs.placement === 'left') {
- anchors.options.class = 'anchorjs-link-left';
- }
- anchors.add(res.join(', '));
- }
- });
- });
- </script>
-
- <script>
- Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
- Fluid.plugins.fancyBox();
- });
- </script>
- <script>Fluid.plugins.imageCaption();</script>
- <script src="/js/local-search.js" ></script>
- <!-- 主题的启动项，将它保持在最底部 -->
- <!-- the boot of the theme, keep it at the bottom -->
- <script src="/js/boot.js" ></script>
-
- <noscript>
- <div class="noscript-warning">Blog works best with JavaScript enabled</div>
- </noscript>
- <!-- hexo injector body_end start -->
- <script defer src="/theme-inject/timeliness.js"></script>
- <!-- hexo injector body_end end --></body>
- </html>
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