ADA-SVR (2/4) add comments and documentation of the functions and test

doc_conf/references.bib

@@ -177,4 +177,19 @@ @article{liuFastPowerfulConditional2021
   archiveprefix = {arxiv},
   keywords = {Statistics - Methodology},
   file = {/home/ahmad/Zotero/storage/8HRQZX3H/Liu et al. - 2021 - Fast and Powerful Conditional Randomization Testin.pdf;/home/ahmad/Zotero/storage/YFNDKN2B/2006.html}
+}
+
+@article{gaonkar_deriving_2012,
+	title = {Deriving statistical significance maps for {SVM} based image classification and group comparisons},
+	volume = {15},
+	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703958/},
+	pages = {723--730},
+	number = {0},
+	journaltitle = {Medical image computing and computer-assisted intervention : {MICCAI} ... International Conference on Medical Image Computing and Computer-Assisted Intervention},
+	journal = {Med Image Comput Comput Assist Interv},
+	author = {Gaonkar, Bilwaj and Davatzikos, Christos},
+	urldate = {2024-12-16},
+	year = {2012},
+	pmid = {23285616},
+	pmcid = {PMC3703958},
 }

docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt

@@ -554,9 +554,9 @@ randomization.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (1 minutes 7.791 seconds)
+   **Total running time of the script:** (1 minutes 5.235 seconds)
 
-**Estimated memory usage:**  710 MB
+**Estimated memory usage:**  704 MB
 
 
 .. _sphx_glr_download_auto_examples_plot_2D_simulation_example.py:

docs/_sources/auto_examples/plot_dcrt_example.rst.txt

@@ -162,7 +162,7 @@ Plotting the comparison
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (1 minutes 3.192 seconds)
+   **Total running time of the script:** (1 minutes 3.346 seconds)
 
 **Estimated memory usage:**  640 MB
 

docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt

@@ -491,7 +491,7 @@ Analyze the results
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 8.885 seconds)
+   **Total running time of the script:** (0 minutes 8.310 seconds)
 
 **Estimated memory usage:**  625 MB
 

docs/_sources/auto_examples/plot_fmri_data_example.rst.txt

@@ -182,7 +182,7 @@ You may choose a subject in [1, 2, 3, 4, 5, 6]. By default subject=2.
     [fetch_single_file]  ...done. (0 seconds, 0 min)
 
     [fetch_single_file] Downloading data from http://data.pymvpa.org/datasets/haxby2001/subj2-2010.01.14.tar.gz ...
-    [_chunk_report_]     Downloaded 161644544 of 291168628 bytes (55.5%%,    0.8s remaining)
+    [_chunk_report_]     Downloaded 133627904 of 291168628 bytes (45.9%%,    1.2s remaining)
     [fetch_single_file]  ...done. (2 seconds, 0 min)
 
     [uncompress_file] Extracting data from /home/runner/nilearn_data/haxby2001/9cabe068089e791ef0c5fe930fc20e30/subj2-2010.01.14.tar.gz...
@@ -287,8 +287,8 @@ Now, we compute p-values thanks to permutation tests applied to
 
  .. code-block:: none
 
-    [Parallel(n_jobs=1)]: Done  49 tasks      | elapsed:    1.5s
-    [Parallel(n_jobs=1)]: Done 199 tasks      | elapsed:    6.6s
+    [Parallel(n_jobs=1)]: Done  49 tasks      | elapsed:    2.1s
+    [Parallel(n_jobs=1)]: Done 199 tasks      | elapsed:    8.2s
 
 
 
@@ -369,7 +369,7 @@ However you might benefit from clustering randomization taking
  .. code-block:: none
 
     [Parallel(n_jobs=2)]: Using backend LokyBackend with 2 concurrent workers.
-    [Parallel(n_jobs=2)]: Done   5 out of   5 | elapsed:   32.3s finished
+    [Parallel(n_jobs=2)]: Done   5 out of   5 | elapsed:   33.9s finished
 
 
 
@@ -614,9 +614,9 @@ spurious discoveries.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (1 minutes 22.801 seconds)
+   **Total running time of the script:** (1 minutes 28.482 seconds)
 
-**Estimated memory usage:**  3279 MB
+**Estimated memory usage:**  3332 MB
 
 
 .. _sphx_glr_download_auto_examples_plot_fmri_data_example.py:

docs/_sources/auto_examples/plot_knockoff_aggregation.rst.txt

@@ -205,9 +205,9 @@ Imports needed for this script
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (5 minutes 45.456 seconds)
+   **Total running time of the script:** (5 minutes 39.860 seconds)
 
-**Estimated memory usage:**  809 MB
+**Estimated memory usage:**  799 MB
 
 
 .. _sphx_glr_download_auto_examples_plot_knockoff_aggregation.py:

docs/_sources/auto_examples/plot_variable_importance_classif.rst.txt

@@ -176,7 +176,7 @@ Visualize the data
  .. code-block:: none
 
 
-    [<matplotlib.axis.YTick object at 0x7fcb1addca40>, <matplotlib.axis.YTick object at 0x7fcb1adde2a0>, <matplotlib.axis.YTick object at 0x7fca47b25880>, <matplotlib.axis.YTick object at 0x7fca47b26630>, <matplotlib.axis.YTick object at 0x7fca47b247a0>, <matplotlib.axis.YTick object at 0x7fca47b269f0>, <matplotlib.axis.YTick object at 0x7fca47b24fb0>, <matplotlib.axis.YTick object at 0x7fcb1bce1a60>, <matplotlib.axis.YTick object at 0x7fcb1bce0200>, <matplotlib.axis.YTick object at 0x7fca47b24530>]
+    [<matplotlib.axis.YTick object at 0x7f38bac848c0>, <matplotlib.axis.YTick object at 0x7f38b9cd64e0>, <matplotlib.axis.YTick object at 0x7f38b9cee900>, <matplotlib.axis.YTick object at 0x7f38b9cef290>, <matplotlib.axis.YTick object at 0x7f38b9cd4740>, <matplotlib.axis.YTick object at 0x7f38b9cec8f0>, <matplotlib.axis.YTick object at 0x7f38b9cecf80>, <matplotlib.axis.YTick object at 0x7f38b9cecdd0>, <matplotlib.axis.YTick object at 0x7f38b9c059d0>, <matplotlib.axis.YTick object at 0x7f38b9ceef00>]
 
 
 
@@ -422,14 +422,14 @@ the features.
  .. code-block:: none
 
 
-    <matplotlib.legend.Legend object at 0x7fcb1a06dd00>
+    <matplotlib.legend.Legend object at 0x7f38b887ff50>
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 43.179 seconds)
+   **Total running time of the script:** (0 minutes 44.394 seconds)
 
 **Estimated memory usage:**  621 MB
 

docs/_sources/auto_examples/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**10:11.305** total execution time for 6 files **from auto_examples**:
+**10:09.627** total execution time for 6 files **from auto_examples**:
 
 .. container::
 
@@ -33,20 +33,20 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_knockoff_aggregation.py` (``plot_knockoff_aggregation.py``)
-     - 05:45.456
-     - 808.7
+     - 05:39.860
+     - 799.2
    * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``plot_fmri_data_example.py``)
-     - 01:22.801
-     - 3279.1
+     - 01:28.482
+     - 3332.4
    * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``plot_2D_simulation_example.py``)
-     - 01:07.791
-     - 710.0
+     - 01:05.235
+     - 703.5
    * - :ref:`sphx_glr_auto_examples_plot_dcrt_example.py` (``plot_dcrt_example.py``)
-     - 01:03.192
-     - 640.2
+     - 01:03.346
+     - 639.5
    * - :ref:`sphx_glr_auto_examples_plot_variable_importance_classif.py` (``plot_variable_importance_classif.py``)
-     - 00:43.179
-     - 620.6
+     - 00:44.394
+     - 620.7
    * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``plot_diabetes_variable_importance_example.py``)
-     - 00:08.885
-     - 624.9
+     - 00:08.310
+     - 624.6

docs/_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**10:11.305** total execution time for 6 files **from all galleries**:
+**10:09.627** total execution time for 6 files **from all galleries**:
 
 .. container::
 
@@ -33,20 +33,20 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_knockoff_aggregation.py` (``../examples/plot_knockoff_aggregation.py``)
-     - 05:45.456
-     - 808.7
+     - 05:39.860
+     - 799.2
    * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``../examples/plot_fmri_data_example.py``)
-     - 01:22.801
-     - 3279.1
+     - 01:28.482
+     - 3332.4
    * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``../examples/plot_2D_simulation_example.py``)
-     - 01:07.791
-     - 710.0
+     - 01:05.235
+     - 703.5
    * - :ref:`sphx_glr_auto_examples_plot_dcrt_example.py` (``../examples/plot_dcrt_example.py``)
-     - 01:03.192
-     - 640.2
+     - 01:03.346
+     - 639.5
    * - :ref:`sphx_glr_auto_examples_plot_variable_importance_classif.py` (``../examples/plot_variable_importance_classif.py``)
-     - 00:43.179
-     - 620.6
+     - 00:44.394
+     - 620.7
    * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``../examples/plot_diabetes_variable_importance_example.py``)
-     - 00:08.885
-     - 624.9
+     - 00:08.310
+     - 624.6

docs/_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.dev1+geccd3d8',
+    VERSION: '0.1.dev1+g14c546e',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/api.html

@@ -5,15 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>API Documentation &#8212; HiDimStat 0.1.dev1+geccd3d8 documentation</title>
+    <title>API Documentation &#8212; HiDimStat 0.1.dev1+g14c546e documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/bootstrap-sphinx.css?v=284a2d1d" />
     <link rel="stylesheet" type="text/css" href="_static/style.css?v=fbda0898" />
     <link rel="stylesheet" type="text/css" href="_static/sg_gallery.css?v=d2d258e8" />
     <link rel="stylesheet" type="text/css" href="_static/sg_gallery-binder.css?v=f4aeca0c" />
     <link rel="stylesheet" type="text/css" href="_static/sg_gallery-dataframe.css?v=2082cf3c" />
     <link rel="stylesheet" type="text/css" href="_static/sg_gallery-rendered-html.css?v=1277b6f3" />
-    <script src="_static/documentation_options.js?v=ddc88f42"></script>
+    <script src="_static/documentation_options.js?v=e55f5a7a"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />

docs/auto_examples/index.html

@@ -5,15 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Examples Gallery &#8212; HiDimStat 0.1.dev1+geccd3d8 documentation</title>
+    <title>Examples Gallery &#8212; HiDimStat 0.1.dev1+g14c546e documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css?v=284a2d1d" />
     <link rel="stylesheet" type="text/css" href="../_static/style.css?v=fbda0898" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css?v=2082cf3c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
-    <script src="../_static/documentation_options.js?v=ddc88f42"></script>
+    <script src="../_static/documentation_options.js?v=e55f5a7a"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>

docs/auto_examples/plot_2D_simulation_example.html

@@ -5,15 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Support recovery on simulated data (2D) &#8212; HiDimStat 0.1.dev1+geccd3d8 documentation</title>
+    <title>Support recovery on simulated data (2D) &#8212; HiDimStat 0.1.dev1+g14c546e documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css?v=284a2d1d" />
     <link rel="stylesheet" type="text/css" href="../_static/style.css?v=fbda0898" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css?v=2082cf3c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
-    <script src="../_static/documentation_options.js?v=ddc88f42"></script>
+    <script src="../_static/documentation_options.js?v=e55f5a7a"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -475,8 +475,8 @@ <h2>Analysis of the results<a class="headerlink" href="#analysis-of-the-results"
 conservative. In practice, Type-1 Error guarantees seem to hold
 for a lower spatial tolerance. This is an additional benefit of clustering
 randomization.</p>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 7.791 seconds)</p>
-<p><strong>Estimated memory usage:</strong>  710 MB</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 5.235 seconds)</p>
+<p><strong>Estimated memory usage:</strong>  704 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-plot-2d-simulation-example-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">
 <p><a class="reference download internal" download="" href="../_downloads/7d2770a07fbe419760c9ac177df4f69e/plot_2D_simulation_example.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_2D_simulation_example.ipynb</span></code></a></p>

docs/auto_examples/plot_dcrt_example.html

@@ -5,15 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Distilled Conditional Randomization Test (dCRT) using Lasso vs Random Forest learners &#8212; HiDimStat 0.1.dev1+geccd3d8 documentation</title>
+    <title>Distilled Conditional Randomization Test (dCRT) using Lasso vs Random Forest learners &#8212; HiDimStat 0.1.dev1+g14c546e documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css?v=284a2d1d" />
     <link rel="stylesheet" type="text/css" href="../_static/style.css?v=fbda0898" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css?v=2082cf3c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
-    <script src="../_static/documentation_options.js?v=ddc88f42"></script>
+    <script src="../_static/documentation_options.js?v=e55f5a7a"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -210,7 +210,7 @@ <h2>Plotting the comparison<a class="headerlink" href="#plotting-the-comparison"
 <a href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.show.html#matplotlib.pyplot.show" title="matplotlib.pyplot.show" class="sphx-glr-backref-module-matplotlib-pyplot sphx-glr-backref-type-py-function"><span class="n">plt</span><span class="o">.</span><span class="n">show</span></a><span class="p">()</span>
 </pre></div>
 </div>
-<img src="../_images/sphx_glr_plot_dcrt_example_001.png" srcset="../_images/sphx_glr_plot_dcrt_example_001.png" alt="Type-I Error, Power" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 3.192 seconds)</p>
+<img src="../_images/sphx_glr_plot_dcrt_example_001.png" srcset="../_images/sphx_glr_plot_dcrt_example_001.png" alt="Type-I Error, Power" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (1 minutes 3.346 seconds)</p>
 <p><strong>Estimated memory usage:</strong>  640 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-plot-dcrt-example-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">

docs/auto_examples/plot_diabetes_variable_importance_example.html

@@ -5,15 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Variable Importance on diabetes dataset &#8212; HiDimStat 0.1.dev1+geccd3d8 documentation</title>
+    <title>Variable Importance on diabetes dataset &#8212; HiDimStat 0.1.dev1+g14c546e documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css?v=284a2d1d" />
     <link rel="stylesheet" type="text/css" href="../_static/style.css?v=fbda0898" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css?v=2082cf3c" />
     <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
-    <script src="../_static/documentation_options.js?v=ddc88f42"></script>
+    <script src="../_static/documentation_options.js?v=e55f5a7a"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -467,7 +467,7 @@ <h2>Analyze the results<a class="headerlink" href="#analyze-the-results" title="
   ax.set_xticklabels(diabetes.feature_names)
 </pre></div>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 8.885 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 8.310 seconds)</p>
 <p><strong>Estimated memory usage:</strong>  625 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-plot-diabetes-variable-importance-example-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">