[ci skip] Merge pull request #59 from ogrisel/fix-warning-load_seer

Fix a pandas warning in load_seer cf07d74
soda-inria · Jul 3, 2024 · 4716832 · 4716832
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diff --git a/.doctrees/auto_examples/plot_marginal_cumulative_incidence_estimation.doctree b/.doctrees/auto_examples/plot_marginal_cumulative_incidence_estimation.doctree
diff --git a/.doctrees/auto_examples/sg_execution_times.doctree b/.doctrees/auto_examples/sg_execution_times.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/sg_execution_times.doctree b/.doctrees/sg_execution_times.doctree
diff --git a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/_sources/auto_examples/plot_marginal_cumulative_incidence_estimation.rst.txt b/_sources/auto_examples/plot_marginal_cumulative_incidence_estimation.rst.txt
@@ -279,19 +279,19 @@ theoretical CIFs:
 
  .. code-block:: none
 
-    Integrated theoretical any event survival curve in 0.591 s
-    Integrated theoretical cumulative incidence curve for event 1 in 0.653 s
-    GB Incidence for event 1 fit in 0.452 s
+    Integrated theoretical any event survival curve in 0.628 s
+    Integrated theoretical cumulative incidence curve for event 1 in 0.692 s
+    GB Incidence for event 1 fit in 0.479 s
     GB Incidence for event 1 prediction in 0.082 s
-    Aalen-Johansen for event 1 fit in 5.157 s
-    Integrated theoretical cumulative incidence curve for event 2 in 5.333 s
-    GB Incidence for event 2 fit in 0.435 s
+    Aalen-Johansen for event 1 fit in 5.195 s
+    Integrated theoretical cumulative incidence curve for event 2 in 5.388 s
+    GB Incidence for event 2 fit in 0.440 s
     GB Incidence for event 2 prediction in 0.082 s
-    Aalen-Johansen for event 2 fit in 5.185 s
-    Integrated theoretical cumulative incidence curve for event 3 in 5.264 s
-    GB Incidence for event 3 fit in 0.421 s
-    GB Incidence for event 3 prediction in 0.081 s
-    Aalen-Johansen for event 3 fit in 5.235 s
+    Aalen-Johansen for event 2 fit in 5.166 s
+    Integrated theoretical cumulative incidence curve for event 3 in 5.248 s
+    GB Incidence for event 3 fit in 0.429 s
+    GB Incidence for event 3 prediction in 0.082 s
+    Aalen-Johansen for event 3 fit in 5.249 s
 
 
 
@@ -363,19 +363,19 @@ of censoring.
 
  .. code-block:: none
 
-    Integrated theoretical any event survival curve in 0.587 s
-    Integrated theoretical cumulative incidence curve for event 1 in 0.649 s
-    GB Incidence for event 1 fit in 0.470 s
-    GB Incidence for event 1 prediction in 0.097 s
-    Aalen-Johansen for event 1 fit in 5.201 s
-    Integrated theoretical cumulative incidence curve for event 2 in 5.310 s
-    GB Incidence for event 2 fit in 0.440 s
-    GB Incidence for event 2 prediction in 0.086 s
-    Aalen-Johansen for event 2 fit in 5.188 s
-    Integrated theoretical cumulative incidence curve for event 3 in 5.267 s
-    GB Incidence for event 3 fit in 0.411 s
-    GB Incidence for event 3 prediction in 0.082 s
-    Aalen-Johansen for event 3 fit in 5.157 s
+    Integrated theoretical any event survival curve in 0.605 s
+    Integrated theoretical cumulative incidence curve for event 1 in 0.668 s
+    GB Incidence for event 1 fit in 0.449 s
+    GB Incidence for event 1 prediction in 0.083 s
+    Aalen-Johansen for event 1 fit in 5.208 s
+    Integrated theoretical cumulative incidence curve for event 2 in 5.316 s
+    GB Incidence for event 2 fit in 0.446 s
+    GB Incidence for event 2 prediction in 0.081 s
+    Aalen-Johansen for event 2 fit in 5.176 s
+    Integrated theoretical cumulative incidence curve for event 3 in 5.258 s
+    GB Incidence for event 3 fit in 0.420 s
+    GB Incidence for event 3 prediction in 0.083 s
+    Aalen-Johansen for event 3 fit in 5.164 s
 
 
 
@@ -425,15 +425,15 @@ constraint:
 
  .. code-block:: none
 
-    Integrated theoretical any event survival curve in 0.593 s
-    Integrated theoretical cumulative incidence curve for event 1 in 0.655 s
-    GB Incidence for event 1 fit in 0.429 s
-    GB Incidence for event 1 prediction in 0.081 s
-    Integrated theoretical cumulative incidence curve for event 2 in 0.145 s
-    GB Incidence for event 2 fit in 0.434 s
+    Integrated theoretical any event survival curve in 0.600 s
+    Integrated theoretical cumulative incidence curve for event 1 in 0.663 s
+    GB Incidence for event 1 fit in 0.432 s
+    GB Incidence for event 1 prediction in 0.082 s
+    Integrated theoretical cumulative incidence curve for event 2 in 0.147 s
+    GB Incidence for event 2 fit in 0.441 s
     GB Incidence for event 2 prediction in 0.081 s
-    Integrated theoretical cumulative incidence curve for event 3 in 0.145 s
-    GB Incidence for event 3 fit in 0.423 s
+    Integrated theoretical cumulative incidence curve for event 3 in 0.147 s
+    GB Incidence for event 3 fit in 0.424 s
     GB Incidence for event 3 prediction in 0.081 s
 
 
@@ -450,7 +450,7 @@ uncertainty).
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 39.396 seconds)
+   **Total running time of the script:** (0 minutes 39.633 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_marginal_cumulative_incidence_estimation.py:

diff --git a/_sources/auto_examples/sg_execution_times.rst.txt b/_sources/auto_examples/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:39.396** total execution time for 1 file **from auto_examples**:
+**00:39.633** total execution time for 1 file **from auto_examples**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_marginal_cumulative_incidence_estimation.py` (``plot_marginal_cumulative_incidence_estimation.py``)
-     - 00:39.396
+     - 00:39.633
      - 0.0
diff --git a/_sources/sg_execution_times.rst.txt b/_sources/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:39.396** total execution time for 1 file **from all galleries**:
+**00:39.633** total execution time for 1 file **from all galleries**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_marginal_cumulative_incidence_estimation.py` (``../examples/plot_marginal_cumulative_incidence_estimation.py``)
-     - 00:39.396
+     - 00:39.633
      - 0.0
diff --git a/auto_examples/plot_marginal_cumulative_incidence_estimation.html b/auto_examples/plot_marginal_cumulative_incidence_estimation.html
@@ -549,19 +549,19 @@ <h2>CIFs estimated on uncensored data<a class="headerlink" href="#cifs-estimated
 <span class="p">)</span>
 </pre></div>
 </div>
-<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_001.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_001.png" alt="Cause-specific cumulative incidence functions (0.0% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.591 s
-Integrated theoretical cumulative incidence curve for event 1 in 0.653 s
-GB Incidence for event 1 fit in 0.452 s
+<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_001.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_001.png" alt="Cause-specific cumulative incidence functions (0.0% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.628 s
+Integrated theoretical cumulative incidence curve for event 1 in 0.692 s
+GB Incidence for event 1 fit in 0.479 s
 GB Incidence for event 1 prediction in 0.082 s
-Aalen-Johansen for event 1 fit in 5.157 s
-Integrated theoretical cumulative incidence curve for event 2 in 5.333 s
-GB Incidence for event 2 fit in 0.435 s
+Aalen-Johansen for event 1 fit in 5.195 s
+Integrated theoretical cumulative incidence curve for event 2 in 5.388 s
+GB Incidence for event 2 fit in 0.440 s
 GB Incidence for event 2 prediction in 0.082 s
-Aalen-Johansen for event 2 fit in 5.185 s
-Integrated theoretical cumulative incidence curve for event 3 in 5.264 s
-GB Incidence for event 3 fit in 0.421 s
-GB Incidence for event 3 prediction in 0.081 s
-Aalen-Johansen for event 3 fit in 5.235 s
+Aalen-Johansen for event 2 fit in 5.166 s
+Integrated theoretical cumulative incidence curve for event 3 in 5.248 s
+GB Incidence for event 3 fit in 0.429 s
+GB Incidence for event 3 prediction in 0.082 s
+Aalen-Johansen for event 3 fit in 5.249 s
 </pre></div>
 </div>
 </section>
@@ -600,19 +600,19 @@ <h2>CIFs estimated on censored data<a class="headerlink" href="#cifs-estimated-o
 <span class="p">)</span>
 </pre></div>
 </div>
-<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_002.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_002.png" alt="Cause-specific cumulative incidence functions (47.6% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.587 s
-Integrated theoretical cumulative incidence curve for event 1 in 0.649 s
-GB Incidence for event 1 fit in 0.470 s
-GB Incidence for event 1 prediction in 0.097 s
-Aalen-Johansen for event 1 fit in 5.201 s
-Integrated theoretical cumulative incidence curve for event 2 in 5.310 s
-GB Incidence for event 2 fit in 0.440 s
-GB Incidence for event 2 prediction in 0.086 s
-Aalen-Johansen for event 2 fit in 5.188 s
-Integrated theoretical cumulative incidence curve for event 3 in 5.267 s
-GB Incidence for event 3 fit in 0.411 s
-GB Incidence for event 3 prediction in 0.082 s
-Aalen-Johansen for event 3 fit in 5.157 s
+<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_002.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_002.png" alt="Cause-specific cumulative incidence functions (47.6% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.605 s
+Integrated theoretical cumulative incidence curve for event 1 in 0.668 s
+GB Incidence for event 1 fit in 0.449 s
+GB Incidence for event 1 prediction in 0.083 s
+Aalen-Johansen for event 1 fit in 5.208 s
+Integrated theoretical cumulative incidence curve for event 2 in 5.316 s
+GB Incidence for event 2 fit in 0.446 s
+GB Incidence for event 2 prediction in 0.081 s
+Aalen-Johansen for event 2 fit in 5.176 s
+Integrated theoretical cumulative incidence curve for event 3 in 5.258 s
+GB Incidence for event 3 fit in 0.420 s
+GB Incidence for event 3 prediction in 0.083 s
+Aalen-Johansen for event 3 fit in 5.164 s
 </pre></div>
 </div>
 <p>Note that the Aalen-Johansen estimator is unbiased and empirically recovers
@@ -637,15 +637,15 @@ <h2>CIFs estimated on censored data<a class="headerlink" href="#cifs-estimated-o
 <span class="p">)</span>
 </pre></div>
 </div>
-<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_003.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_003.png" alt="Cause-specific cumulative incidence functions (47.6% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.593 s
-Integrated theoretical cumulative incidence curve for event 1 in 0.655 s
-GB Incidence for event 1 fit in 0.429 s
-GB Incidence for event 1 prediction in 0.081 s
-Integrated theoretical cumulative incidence curve for event 2 in 0.145 s
-GB Incidence for event 2 fit in 0.434 s
+<img src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_003.png" srcset="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_003.png" alt="Cause-specific cumulative incidence functions (47.6% censoring), Event 1, Event 2, Event 3" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>Integrated theoretical any event survival curve in 0.600 s
+Integrated theoretical cumulative incidence curve for event 1 in 0.663 s
+GB Incidence for event 1 fit in 0.432 s
+GB Incidence for event 1 prediction in 0.082 s
+Integrated theoretical cumulative incidence curve for event 2 in 0.147 s
+GB Incidence for event 2 fit in 0.441 s
 GB Incidence for event 2 prediction in 0.081 s
-Integrated theoretical cumulative incidence curve for event 3 in 0.145 s
-GB Incidence for event 3 fit in 0.423 s
+Integrated theoretical cumulative incidence curve for event 3 in 0.147 s
+GB Incidence for event 3 fit in 0.424 s
 GB Incidence for event 3 prediction in 0.081 s
 </pre></div>
 </div>
@@ -654,7 +654,7 @@ <h2>CIFs estimated on censored data<a class="headerlink" href="#cifs-estimated-o
 particular large time horizons, where the CIFs are getting flatter. This
 effect diminishes with larger training set sizes (lower epistemic
 uncertainty).</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 39.396 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 39.633 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-plot-marginal-cumulative-incidence-estimation-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../_downloads/2932d6ac7842b6d781c27c5737ae52fa/plot_marginal_cumulative_incidence_estimation.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Jupyter</span> <span class="pre">notebook:</span> <span class="pre">plot_marginal_cumulative_incidence_estimation.ipynb</span></code></a></p>

diff --git a/auto_examples/sg_execution_times.html b/auto_examples/sg_execution_times.html
@@ -339,7 +339,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-auto-examples-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading">#</a></h1>
-<p><strong>00:39.396</strong> total execution time for 1 file <strong>from auto_examples</strong>:</p>
+<p><strong>00:39.633</strong> total execution time for 1 file <strong>from auto_examples</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -361,7 +361,7 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="plot_marginal_cumulative_incidence_estimation.html#sphx-glr-auto-examples-plot-marginal-cumulative-incidence-estimation-py"><span class="std std-ref">Estimating marginal cumulative incidence functions</span></a> (<code class="docutils literal notranslate"><span class="pre">plot_marginal_cumulative_incidence_estimation.py</span></code>)</p></td>
-<td><p>00:39.396</p></td>
+<td><p>00:39.633</p></td>
 <td><p>0.0</p></td>
 </tr>
 </tbody>

diff --git a/searchindex.js b/searchindex.js
diff --git a/sg_execution_times.html b/sg_execution_times.html
@@ -339,7 +339,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading">#</a></h1>
-<p><strong>00:39.396</strong> total execution time for 1 file <strong>from all galleries</strong>:</p>
+<p><strong>00:39.633</strong> total execution time for 1 file <strong>from all galleries</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -361,7 +361,7 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="auto_examples/plot_marginal_cumulative_incidence_estimation.html#sphx-glr-auto-examples-plot-marginal-cumulative-incidence-estimation-py"><span class="std std-ref">Estimating marginal cumulative incidence functions</span></a> (<code class="docutils literal notranslate"><span class="pre">../examples/plot_marginal_cumulative_incidence_estimation.py</span></code>)</p></td>
-<td><p>00:39.396</p></td>
+<td><p>00:39.633</p></td>
 <td><p>0.0</p></td>
 </tr>
 </tbody>