MRG: Better docstring for clustering & stats (mne-tools#4743)

* DOC: Better docstring * FIX: Fix docs * ENH: Reorganize * DOC: Many updates * FIX: Fix docstrings * FIX: Fix for doctest * ENH: Plot each section * FIX: Use nearest * FIX: Address comments * STY: Cleaner breaks * FIX: Fix CircleCI check * FIX: Address comments * FIX: Revert CircleCI
codetriage-readme-bot · Nov 16, 2017 · 14e8f60 · 14e8f60
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diff --git a/doc/_static/style.css b/doc/_static/style.css
@@ -280,4 +280,11 @@ h4.list-group-item-heading {
   .collapse.in{
       display:block !important;
   }
-}
+}
+
+.skinnytable {
+    width: auto;
+}
+.skinnytable thead {
+    border-bottom: 1px solid black;
+}
diff --git a/doc/conf.py b/doc/conf.py
@@ -277,16 +277,17 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'python': ('http://docs.python.org', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy-dev', None),
-    'scipy': ('http://scipy.github.io/devdocs', None),
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy-dev', None),
+    'scipy': ('https://scipy.github.io/devdocs', None),
     'matplotlib': ('http://matplotlib.org', None),
     'sklearn': ('http://scikit-learn.org/stable', None),
     'mayavi': ('http://docs.enthought.com/mayavi/mayavi', None),
     'nibabel': ('http://nipy.org/nibabel', None),
     'nilearn': ('http://nilearn.github.io', None),
     'surfer': ('https://pysurfer.github.io/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
+    'statsmodels': ('http://www.statsmodels.org/stable/', None),
 }
 
 examples_dirs = ['../examples', '../tutorials']

diff --git a/doc/documentation.rst b/doc/documentation.rst
@@ -142,6 +142,7 @@ There are also **examples**, which contain a short use-case to highlight MNE-fun
     auto_tutorials/plot_modifying_data_inplace.rst
     auto_tutorials/plot_ecog.rst
     manual/memory.rst
+    manual/migrating.rst
 
 .. raw:: html
 
@@ -464,7 +465,7 @@ There are also **examples**, which contain a short use-case to highlight MNE-fun
       <div class="panel panel-default">
         <div class="panel-heading">
           <h4 class="panel-title">
-            <a data-toggle="collapse" href="#collapse_statistics">Statistics in sensor- and source-space</a>
+            <a data-toggle="collapse" href="#collapse_statistics">Statistics</a>
           </h4>
         </div>
         <div id="collapse_statistics" class="panel-collapse collapse">
@@ -476,14 +477,13 @@ There are also **examples**, which contain a short use-case to highlight MNE-fun
 .. toctree::
     :maxdepth: 1
 
-    manual/statistics.rst
+    auto_tutorials/plot_background_statistics.rst
 
 **Sensor Space**
 
 .. toctree::
     :maxdepth: 1
 
-    auto_tutorials/plot_stats_cluster_methods.rst
     auto_tutorials/plot_stats_spatio_temporal_cluster_sensors.rst
     auto_tutorials/plot_stats_cluster_1samp_test_time_frequency.rst
     auto_tutorials/plot_stats_cluster_time_frequency.rst
@@ -670,6 +670,9 @@ There are also **examples**, which contain a short use-case to highlight MNE-fun
     manual/gui/browse.rst
     manual/appendix/bem_model.rst
     manual/appendix/c_misc.rst
+    manual/appendix/c_release_notes.rst
+    manual/appendix/c_EULA.rst
+    manual/appendix/martinos.rst
 
 **MNE-MATLAB**
 

diff --git a/doc/manual/index.rst b/doc/manual/index.rst
diff --git a/doc/manual/statistics.rst b/doc/manual/statistics.rst
diff --git a/doc/python_reference.rst b/doc/python_reference.rst
@@ -873,6 +873,8 @@ Connectivity Estimation
    phase_slope_index
 
 
+.. _api_reference_statistics:
+
 Statistics
 ==========
 
@@ -884,33 +886,52 @@ Statistics
 
 .. currentmodule:: mne.stats
 
+Parametric statistics (see :mod:`scipy.stats` and :mod:`statsmodels` for more
+options):
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
+   ttest_1samp_no_p
+   f_oneway
+   f_mway_rm
+   f_threshold_mway_rm
+   linear_regression
+   linear_regression_raw
+
+Mass-univariate multiple comparison correction:
+
 .. autosummary::
    :toctree: generated/
    :template: function.rst
 
    bonferroni_correction
    fdr_correction
+
+Non-parametric (clustering) resampling methods:
+
+.. autosummary::
+   :toctree: generated/
+   :template: function.rst
+
    permutation_cluster_test
    permutation_cluster_1samp_test
    permutation_t_test
    spatio_temporal_cluster_test
    spatio_temporal_cluster_1samp_test
-   ttest_1samp_no_p
-   linear_regression
-   linear_regression_raw
-   f_oneway
-   f_mway_rm
-   f_threshold_mway_rm
    summarize_clusters_stc
 
-Functions to compute neighbor/adjacency matrices for cluster-level statistics:
+Compute ``connectivity`` matrices for cluster-level statistics:
 
 .. currentmodule:: mne
 
 .. autosummary::
    :toctree: generated/
    :template: function.rst
 
+   channels.find_ch_connectivity
+   channels.read_ch_connectivity
    spatial_dist_connectivity
    spatial_src_connectivity
    spatial_tris_connectivity

diff --git a/doc/whats_new.rst b/doc/whats_new.rst
@@ -40,6 +40,8 @@ Bug
 
 - Fix bug in :meth:`mne.io.Raw.plot` to correctly display event types when annotations are present by `Clemens Brunner`_
 
+- Fix bug in :func:`mne.stats.spatio_temporal_cluster_test` default value for ``threshold`` is now calculated based on the array sizes in ``X``, by `Eric Larson`_
+
 API
 ~~~
 

diff --git a/examples/datasets/plot_spm_faces_dataset.py b/examples/datasets/plot_spm_faces_dataset.py
@@ -1,4 +1,3 @@
-# doc:slow-example
 """
 ==========================================
 From raw data to dSPM on SPM Faces dataset
-Original file line number
+Diff line change
@@ Expand Up / @@ -40,6 +40,8 @@ Bug @@
     - Fix bug in :meth:`mne.io.Raw.plot` to correctly display event types when annotations are present by `Clemens Brunner`_
+    - Fix bug in :func:`mne.stats.spatio_temporal_cluster_test` default value for ``threshold`` is now calculated based on the array sizes in ``X``, by `Eric Larson`_
     API
     ~~~
@@ Expand Down @@