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            <h1 id="seo-header">COXPH绘制ROC曲线</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><a href="https://occdn.limour.top/2112.html">conda activate ggsurvplot</a></li>
<li># conda install -c conda-forge r-pec -y</li>
<li>conda install -c conda-forge r-survivalroc -y</li>
<li># conda install -c conda-forge r-ggsci -y</li>
<li># conda install -c conda-forge r-scales -y</li>
<li>install.packages(‘nomogramFormula’)</li>
</ul>
<h2 id="整理数据"><a href="#整理数据" class="headerlink" title="整理数据"></a>整理数据</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><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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../A_ref_A_fiig.3_A_B/clinical.rds&#x27;</span><span class="hljs-punctuation">)</span><br>table<span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>PSA<span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-punctuation">[</span><span class="hljs-number">0</span> <span class="hljs-operator">&lt;</span> clinical<span class="hljs-operator">$</span>PSA <span class="hljs-operator">&amp;</span> clinical<span class="hljs-operator">$</span>PSA<span class="hljs-operator">&lt;</span><span class="hljs-number">40</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>clinical<span class="hljs-operator">$</span>PSA <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>PSA<span class="hljs-punctuation">)</span><br>dat <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../COXPH/data/PRAD.rds&#x27;</span><span class="hljs-punctuation">)</span><br>dat<span class="hljs-operator">$</span>meta <span class="hljs-operator">&lt;-</span> dat<span class="hljs-operator">$</span>meta<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>y <span class="hljs-operator">&lt;-</span> Surv<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_time<span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_status <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>y <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> y<span class="hljs-punctuation">)</span><br>table<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>T2vs3 <span class="hljs-operator">&lt;-</span> 0<br>df<span class="hljs-operator">$</span>T2vs3<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span><span class="hljs-built_in">T</span> <span class="hljs-operator">%in%</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;T2a&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;T2b&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;T2c&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-number">1</span><br>table<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>N<span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>N0vs1 <span class="hljs-operator">&lt;-</span> 0<br>df<span class="hljs-operator">$</span>N0vs1<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>N <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;N0&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-number">1</span><br>df<br>saveRDS<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;clinical.rds&#x27;</span><span class="hljs-punctuation">)</span><br>coxmf <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Surv(time, status==1)~PSA+Age+T2vs3+N0vs1+GS&quot;</span><span class="hljs-punctuation">)</span><br>coxmf<br></code></pre></td></tr></table></figure>

<h2 id="计算C-index"><a href="#计算C-index" class="headerlink" title="计算C-index"></a>计算C-index</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></pre></td><td class="code"><pre><code class="hljs R">res.cox <span class="hljs-operator">&lt;-</span> coxph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf<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">&lt;-</span> summary<span class="hljs-punctuation">(</span>res.cox<span class="hljs-punctuation">)</span><br>Ci <span class="hljs-operator">&lt;-</span> tmp_res<span class="hljs-operator">$</span>concordance<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;C&#x27;</span><span class="hljs-punctuation">]</span><br>Ci_se <span class="hljs-operator">&lt;-</span> tmp_res<span class="hljs-operator">$</span>concordance<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;se(C)&#x27;</span><span class="hljs-punctuation">]</span><br><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>Ci<span class="hljs-operator">-</span><span class="hljs-number">1.96</span><span class="hljs-operator">*</span>Ci_se<span class="hljs-punctuation">,</span>Ci<span class="hljs-operator">+</span><span class="hljs-number">1.96</span><span class="hljs-operator">*</span>Ci_se<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="基于survivalROC绘制ROC曲线"><a href="#基于survivalROC绘制ROC曲线" class="headerlink" title="基于survivalROC绘制ROC曲线"></a>基于survivalROC绘制ROC曲线</h2><h3 id="预测生存概率"><a href="#预测生存概率" class="headerlink" title="预测生存概率"></a>预测生存概率</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></pre></td><td class="code"><pre><code class="hljs R">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>f2 <span class="hljs-operator">&lt;-</span> cph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf<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>df<span class="hljs-operator">$</span>`<span class="hljs-number">1</span><span class="hljs-operator">-</span>year` &lt;- predictSurvProb(f2,newdata=df,times=1*12)<br>df$`3<span class="hljs-operator">-</span>year` &lt;- predictSurvProb(f2,newdata=df,times=3*12)<br>df$`5<span class="hljs-operator">-</span>year` &lt;- predictSurvProb(f2,newdata=df,times=5*12)<br>df<br></code></pre></td></tr></table></figure>

<h3 id="计算ROC曲线"><a href="#计算ROC曲线" class="headerlink" title="计算ROC曲线"></a>计算ROC曲线</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></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># year1 &lt;- survivalROC(Stime=df$time,##生存时间</span><br><span class="hljs-comment">#                      status=df$status,## 终止事件</span><br><span class="hljs-comment">#                      marker=df$`1-year`, ## marker value    </span><br><span class="hljs-comment">#                      predict.time = 1*12,## 预测时间截点</span><br><span class="hljs-comment">#                      span = 0.25*nobs^(-0.20))##span,NNE法的namda</span><br>year1 <span class="hljs-operator">&lt;-</span> survivalROC<span class="hljs-punctuation">(</span>Stime<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span><span class="hljs-comment">##生存时间</span><br>                     status<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><span class="hljs-comment">## 终止事件</span><br>                     marker<span class="hljs-operator">=</span><span class="hljs-operator">-</span>df<span class="hljs-operator">$</span>`<span class="hljs-number">1</span><span class="hljs-operator">-</span>year`, ## marker value    <br>                     predict.time = 1*12,## 预测时间截点<br>                     method=&quot;KM&quot;)<br>year3 &lt;- survivalROC(Stime=df$time,##生存时间<br>                     status=df$status,## 终止事件<br>                     marker=-df$`3<span class="hljs-operator">-</span>year`, ## marker value    <br>                     predict.time = 3*12,## 预测时间截点<br>                     method=&quot;KM&quot;)<br>year5 &lt;- survivalROC(Stime=df$time,##生存时间<br>                     status=df$status,## 终止事件<br>                     marker=-df$`5<span class="hljs-operator">-</span>year`, ## marker value    <br>                     predict.time = 5*12,## 预测时间截点<br>                     method=&quot;KM&quot;)<br></code></pre></td></tr></table></figure>

<h3 id="绘制ROC曲线"><a href="#绘制ROC曲线" class="headerlink" title="绘制ROC曲线"></a>绘制ROC曲线</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></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>ggsci<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;scales&quot;</span><span class="hljs-punctuation">)</span><br>pal_nejm<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;default&quot;</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">&quot;default&quot;</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> <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>year1<span class="hljs-operator">$</span>FP<span class="hljs-punctuation">,</span> year1<span class="hljs-operator">$</span>TP<span class="hljs-punctuation">,</span> <span class="hljs-comment">## x=FP,y=TP</span><br>     type<span class="hljs-operator">=</span><span class="hljs-string">&quot;l&quot;</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##线条设置</span><br>     xlim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ylim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>   <br>     xlab<span class="hljs-operator">=</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;FP&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##连接</span><br>     ylab<span class="hljs-operator">=</span><span class="hljs-string">&quot;TP&quot;</span><span class="hljs-punctuation">,</span><br>     main<span class="hljs-operator">=</span><span class="hljs-string">&quot;Time dependent ROC&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-comment">## \n换行符</span><br>abline<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;gray&quot;</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-comment">##线条颜色</span><br>lines<span class="hljs-punctuation">(</span>year3<span class="hljs-operator">$</span>FP<span class="hljs-punctuation">,</span> year3<span class="hljs-operator">$</span>TP<span class="hljs-punctuation">,</span> type<span class="hljs-operator">=</span><span class="hljs-string">&quot;l&quot;</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">,</span>xlim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ylim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>lines<span class="hljs-punctuation">(</span>year5<span class="hljs-operator">$</span>FP<span class="hljs-punctuation">,</span> year5<span class="hljs-operator">$</span>TP<span class="hljs-punctuation">,</span> type<span class="hljs-operator">=</span><span class="hljs-string">&quot;l&quot;</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#E18727FF&quot;</span><span class="hljs-punctuation">,</span>xlim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ylim<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-number">0.6</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.2</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">&quot;AUC of 1-year =&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>year1<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 3-year =&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>year3<span class="hljs-operator">$</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-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 5-year =&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>year5<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-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 x.intersp<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> y.intersp<span class="hljs-operator">=</span><span class="hljs-number">0.8</span><span class="hljs-punctuation">,</span><br>                 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>col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;#E18727FF&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 bty <span class="hljs-operator">=</span> <span class="hljs-string">&quot;n&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-comment"># bty框的类型</span><br>                 seg.len<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>cex<span class="hljs-operator">=</span><span class="hljs-number">0.8</span><span class="hljs-punctuation">)</span><span class="hljs-comment"># </span><br></code></pre></td></tr></table></figure>

<h2 id="基于timeROC绘制ROC曲线"><a href="#基于timeROC绘制ROC曲线" class="headerlink" title="基于timeROC绘制ROC曲线"></a>基于timeROC绘制ROC曲线</h2><h3 id="预测风险得分（前面先预测生存概率）"><a href="#预测风险得分（前面先预测生存概率）" class="headerlink" title="预测风险得分（前面先预测生存概率）"></a>预测风险得分（前面先预测生存概率）</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>nomogramFormula<span class="hljs-punctuation">)</span><br>surv <span class="hljs-operator">&lt;-</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>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">&quot;dd&quot;</span><span class="hljs-punctuation">)</span> <br>nom <span class="hljs-operator">&lt;-</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">&#123;</span>surv<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">&#125;</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">&#123;</span>surv<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">&#125;</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">&#123;</span>surv<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">&#125;</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">&quot;1-year Disease-free Probability&quot;</span><span class="hljs-punctuation">,</span><br>                                        <span class="hljs-string">&quot;3-year Disease-free Probability&quot;</span><span class="hljs-punctuation">,</span><br>                                        <span class="hljs-string">&quot;5-year Disease-free Probability&quot;</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">6</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>nom<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<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">results <span class="hljs-operator">&lt;-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom<span class="hljs-punctuation">)</span><br>df<span class="hljs-operator">$</span>points <span class="hljs-operator">&lt;-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>df<span class="hljs-punctuation">)</span><br>df<br></code></pre></td></tr></table></figure>

<h3 id="计算ROC曲线-1"><a href="#计算ROC曲线-1" class="headerlink" title="计算ROC曲线"></a>计算ROC曲线</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></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># years &lt;- timeROC(T=df$time,delta=df$status,</span><br><span class="hljs-comment">#                   marker=df$points,cause=1,</span><br><span class="hljs-comment">#                   weighting=&quot;cox&quot;,</span><br><span class="hljs-comment"># #                   other_markers=as.matrix(df$`1-year`),</span><br><span class="hljs-comment">#                   times=12*c(1,3,5), ROC=T)</span><br>years <span class="hljs-operator">&lt;-</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">$</span>points<span class="hljs-punctuation">,</span>cause<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>                      weighting<span class="hljs-operator">=</span><span class="hljs-string">&quot;marginal&quot;</span><span class="hljs-punctuation">,</span><br>    <span class="hljs-comment">#                   other_markers=as.matrix(df$`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>years<br></code></pre></td></tr></table></figure>

<h3 id="构造AUC描述"><a href="#构造AUC描述" class="headerlink" title="构造AUC描述"></a>构造AUC描述</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></pre></td><td class="code"><pre><code class="hljs R">auc.ci <span class="hljs-operator">&lt;-</span> confint<span class="hljs-punctuation">(</span>years<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>auc.ci <span class="hljs-operator">&lt;-</span> auc.ci<span class="hljs-operator">$</span>CI_AUC<br>auc.ci<br> <br>years.auc1 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years<span class="hljs-operator">$</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">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc.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">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc.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">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br>years.auc2 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br>years.auc3 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years<span class="hljs-operator">$</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">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc.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">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc.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">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="绘制ROC曲线-1"><a href="#绘制ROC曲线-1" class="headerlink" title="绘制ROC曲线"></a>绘制ROC曲线</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></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>years<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">&quot;Time dependent ROC&quot;</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">)</span>        <br>plot<span class="hljs-punctuation">(</span>years<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">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>years<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">&quot;#E18727FF&quot;</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;bottomright&quot;</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">&quot;AUC of 1-year =&quot;</span><span class="hljs-punctuation">,</span>years.auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 3-year =&quot;</span><span class="hljs-punctuation">,</span>years.auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 5-year =&quot;</span><span class="hljs-punctuation">,</span>years.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">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#E18727FF&quot;</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="对两个模型的ROC曲线进行检验"><a href="#对两个模型的ROC曲线进行检验" class="headerlink" title="对两个模型的ROC曲线进行检验"></a>对两个模型的ROC曲线进行检验</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs R">compare<span class="hljs-punctuation">(</span>model1_years<span class="hljs-punctuation">,</span>model2years<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>

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