diff --git a/doc_conf/api.rst b/doc_conf/api.rst index 885873f3..13937444 100644 --- a/doc_conf/api.rst +++ b/doc_conf/api.rst @@ -26,7 +26,8 @@ Functions knockoff_aggregation model_x_knockoff multivariate_1D_simulation - permutation_test_cv + permutation_test + permutation_test_pval reid standardized_svr zscore_from_pval diff --git a/doc_conf/references.bib b/doc_conf/references.bib index 4b8a42a4..a7182329 100644 --- a/doc_conf/references.bib +++ b/doc_conf/references.bib @@ -179,6 +179,24 @@ @article{liuFastPowerfulConditional2021 file = {/home/ahmad/Zotero/storage/8HRQZX3H/Liu et al. - 2021 - Fast and Powerful Conditional Randomization Testin.pdf;/home/ahmad/Zotero/storage/YFNDKN2B/2006.html} } +@book{westfall1993resampling, + title={Resampling-based multiple testing: Examples and methods for p-value adjustment}, + author={Westfall, Peter H and Young, S Stanley}, + volume={279}, + year={1993}, + publisher={John Wiley \& Sons} +} + +@article{hirschhorn2005genome, + title={Genome-wide association studies for common diseases and complex traits}, + author={Hirschhorn, Joel N and Daly, Mark J}, + journal={Nature reviews genetics}, + volume={6}, + number={2}, + pages={95--108}, + year={2005}, + publisher={Nature Publishing Group UK London} +} @article{gaonkar_deriving_2012, title = {Deriving statistical significance maps for {SVM} based image classification and group comparisons}, volume = {15}, @@ -192,4 +210,4 @@ @article{gaonkar_deriving_2012 year = {2012}, pmid = {23285616}, pmcid = {PMC3703958}, -} \ No newline at end of file +} diff --git a/docs/_downloads/06bb0f682e15138dfd659b791a14e9c6/plot_variable_importance_classif.zip b/docs/_downloads/06bb0f682e15138dfd659b791a14e9c6/plot_variable_importance_classif.zip index 2b0accb6..7d6858c0 100644 Binary files a/docs/_downloads/06bb0f682e15138dfd659b791a14e9c6/plot_variable_importance_classif.zip and b/docs/_downloads/06bb0f682e15138dfd659b791a14e9c6/plot_variable_importance_classif.zip differ diff 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a/docs/_downloads/707d94040f5ada342e781499193f46f1/plot_diabetes_variable_importance_example.zip b/docs/_downloads/707d94040f5ada342e781499193f46f1/plot_diabetes_variable_importance_example.zip index 680bd64c..d4c70394 100644 Binary files a/docs/_downloads/707d94040f5ada342e781499193f46f1/plot_diabetes_variable_importance_example.zip and b/docs/_downloads/707d94040f5ada342e781499193f46f1/plot_diabetes_variable_importance_example.zip differ diff --git a/docs/_downloads/e08c0f6d4aade0f0eaf8ba56dbbfd9c9/plot_2D_simulation_example.zip b/docs/_downloads/e08c0f6d4aade0f0eaf8ba56dbbfd9c9/plot_2D_simulation_example.zip index b21d2547..23329520 100644 Binary files a/docs/_downloads/e08c0f6d4aade0f0eaf8ba56dbbfd9c9/plot_2D_simulation_example.zip and b/docs/_downloads/e08c0f6d4aade0f0eaf8ba56dbbfd9c9/plot_2D_simulation_example.zip differ diff --git a/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt b/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt index 7326240c..b2bc3678 100644 --- a/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt +++ b/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 4.127 seconds) + **Total running time of the script:** (1 minutes 9.317 seconds) -**Estimated memory usage:** 721 MB +**Estimated memory usage:** 722 MB .. _sphx_glr_download_auto_examples_plot_2D_simulation_example.py: diff --git a/docs/_sources/auto_examples/plot_dcrt_example.rst.txt b/docs/_sources/auto_examples/plot_dcrt_example.rst.txt index b0b4fc2d..3642c609 100644 --- a/docs/_sources/auto_examples/plot_dcrt_example.rst.txt +++ b/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 2.837 seconds) + **Total running time of the script:** (1 minutes 2.817 seconds) **Estimated memory usage:** 657 MB diff --git a/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt b/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt index ac5743aa..18359c5e 100644 --- a/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt +++ b/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt @@ -491,9 +491,9 @@ Analyze the results .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 7.962 seconds) + **Total running time of the script:** (0 minutes 8.597 seconds) -**Estimated memory usage:** 642 MB +**Estimated memory usage:** 643 MB .. _sphx_glr_download_auto_examples_plot_diabetes_variable_importance_example.py: diff --git a/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt b/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt index 8656d641..946918db 100644 --- a/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt +++ b/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt @@ -182,8 +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 117604352 of 291168628 bytes (40.4%%, 1.5s remaining) - [_chunk_report_] Downloaded 257982464 of 291168628 bytes (88.6%%, 0.3s remaining) + [_chunk_report_] Downloaded 158646272 of 291168628 bytes (54.5%%, 0.8s 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... @@ -288,8 +287,8 @@ Now, we compute p-values thanks to permutation tests applied to .. code-block:: none - [Parallel(n_jobs=1)]: Done 49 tasks | elapsed: 1.6s - [Parallel(n_jobs=1)]: Done 199 tasks | elapsed: 6.4s + [Parallel(n_jobs=1)]: Done 49 tasks | elapsed: 1.5s + [Parallel(n_jobs=1)]: Done 199 tasks | elapsed: 6.2s @@ -370,7 +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: 31.4s finished + [Parallel(n_jobs=2)]: Done 5 out of 5 | elapsed: 36.0s finished @@ -615,9 +614,9 @@ spurious discoveries. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (1 minutes 21.474 seconds) + **Total running time of the script:** (1 minutes 30.075 seconds) -**Estimated memory usage:** 3366 MB +**Estimated memory usage:** 3168 MB .. _sphx_glr_download_auto_examples_plot_fmri_data_example.py: diff --git a/docs/_sources/auto_examples/plot_knockoff_aggregation.rst.txt b/docs/_sources/auto_examples/plot_knockoff_aggregation.rst.txt index 4c18f04f..c80663b6 100644 --- a/docs/_sources/auto_examples/plot_knockoff_aggregation.rst.txt +++ b/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 31.483 seconds) + **Total running time of the script:** (5 minutes 36.030 seconds) -**Estimated memory usage:** 830 MB +**Estimated memory usage:** 829 MB .. _sphx_glr_download_auto_examples_plot_knockoff_aggregation.py: diff --git a/docs/_sources/auto_examples/plot_variable_importance_classif.rst.txt b/docs/_sources/auto_examples/plot_variable_importance_classif.rst.txt index d6fc9dc7..5bad810c 100644 --- a/docs/_sources/auto_examples/plot_variable_importance_classif.rst.txt +++ b/docs/_sources/auto_examples/plot_variable_importance_classif.rst.txt @@ -176,7 +176,7 @@ Visualize the data .. code-block:: none - [, , , , , , , , , ] + [, , , , , , , , , ] @@ -422,14 +422,14 @@ the features. .. code-block:: none - + .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 43.075 seconds) + **Total running time of the script:** (0 minutes 44.958 seconds) **Estimated memory usage:** 639 MB diff --git a/docs/_sources/auto_examples/sg_execution_times.rst.txt b/docs/_sources/auto_examples/sg_execution_times.rst.txt index 1619a98a..54215732 100644 --- a/docs/_sources/auto_examples/sg_execution_times.rst.txt +++ b/docs/_sources/auto_examples/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**09:50.958** total execution time for 6 files **from auto_examples**: +**10:11.793** 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``) - - 05:31.483 - - 830.3 + - 05:36.030 + - 829.1 * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``plot_fmri_data_example.py``) - - 01:21.474 - - 3366.4 + - 01:30.075 + - 3167.8 * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``plot_2D_simulation_example.py``) - - 01:04.127 - - 721.4 + - 01:09.317 + - 721.7 * - :ref:`sphx_glr_auto_examples_plot_dcrt_example.py` (``plot_dcrt_example.py``) - - 01:02.837 + - 01:02.817 - 657.4 * - :ref:`sphx_glr_auto_examples_plot_variable_importance_classif.py` (``plot_variable_importance_classif.py``) - - 00:43.075 - - 638.7 + - 00:44.958 + - 638.9 * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``plot_diabetes_variable_importance_example.py``) - - 00:07.962 - - 642.4 + - 00:08.597 + - 642.7 diff --git a/docs/_sources/sg_execution_times.rst.txt b/docs/_sources/sg_execution_times.rst.txt index 53c5a0c8..37fb0cbb 100644 --- a/docs/_sources/sg_execution_times.rst.txt +++ b/docs/_sources/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**09:50.958** total execution time for 6 files **from all galleries**: +**10:11.793** 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``) - - 05:31.483 - - 830.3 + - 05:36.030 + - 829.1 * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``../examples/plot_fmri_data_example.py``) - - 01:21.474 - - 3366.4 + - 01:30.075 + - 3167.8 * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``../examples/plot_2D_simulation_example.py``) - - 01:04.127 - - 721.4 + - 01:09.317 + - 721.7 * - :ref:`sphx_glr_auto_examples_plot_dcrt_example.py` (``../examples/plot_dcrt_example.py``) - - 01:02.837 + - 01:02.817 - 657.4 * - :ref:`sphx_glr_auto_examples_plot_variable_importance_classif.py` (``../examples/plot_variable_importance_classif.py``) - - 00:43.075 - - 638.7 + - 00:44.958 + - 638.9 * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``../examples/plot_diabetes_variable_importance_example.py``) - - 00:07.962 - - 642.4 + - 00:08.597 + - 642.7 diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index ceacdb5d..4342f260 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.1.dev1+gf9ff6b9', + VERSION: '0.1.dev1+gd126c6d', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/api.html b/docs/api.html index c37774c1..6d47193c 100644 --- a/docs/api.html +++ b/docs/api.html @@ -5,7 +5,7 @@ - API Documentation — HiDimStat 0.1.dev1+gf9ff6b9 documentation + API Documentation — HiDimStat 0.1.dev1+gd126c6d documentation @@ -13,7 +13,7 @@ - + diff --git a/docs/auto_examples/index.html b/docs/auto_examples/index.html index 7f2cc839..0602b6e4 100644 --- a/docs/auto_examples/index.html +++ b/docs/auto_examples/index.html @@ -5,7 +5,7 @@ - Examples Gallery — HiDimStat 0.1.dev1+gf9ff6b9 documentation + Examples Gallery — HiDimStat 0.1.dev1+gd126c6d documentation @@ -13,7 +13,7 @@ - + diff --git a/docs/auto_examples/plot_2D_simulation_example.html b/docs/auto_examples/plot_2D_simulation_example.html index d94163d8..1921c2ec 100644 --- a/docs/auto_examples/plot_2D_simulation_example.html +++ b/docs/auto_examples/plot_2D_simulation_example.html @@ -5,7 +5,7 @@ - Support recovery on simulated data (2D) — HiDimStat 0.1.dev1+gf9ff6b9 documentation + Support recovery on simulated data (2D) — HiDimStat 0.1.dev1+gd126c6d documentation @@ -13,7 +13,7 @@ - + @@ -475,8 +475,8 @@

Analysis of the results -

Total running time of the script: (1 minutes 4.127 seconds)

-

Estimated memory usage: 721 MB

+

Total running time of the script: (1 minutes 9.317 seconds)

+

Estimated memory usage: 722 MB

 -Type-I Error, Power

Total running time of the script: (1 minutes 2.837 seconds)

+Type-I Error, Power

Total running time of the script: (1 minutes 2.817 seconds)

Estimated memory usage: 657 MB