Skip to content

Commit

Permalink
further documentation updates
Browse files Browse the repository at this point in the history
  • Loading branch information
Andre Marquand committed Jul 27, 2021
1 parent 969fd1c commit 89f5571
Show file tree
Hide file tree
Showing 18 changed files with 32 additions and 22 deletions.
Binary file modified doc/build/doctrees/environment.pickle
Binary file not shown.
Binary file modified doc/build/doctrees/pages/tutorial_HBR.doctree
Binary file not shown.
2 changes: 1 addition & 1 deletion doc/build/html/_modules/bayesreg.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/fileio.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/gp.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/normative_parallel.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/rfa.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/_modules/trendsurf.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
9 changes: 7 additions & 2 deletions doc/build/html/_sources/pages/tutorial_HBR.rst.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
Predictive Clinical Neuroscience Toolkit
Hierarchical Bayesian Regression
======================================================================================

Hierarchical Bayesian Regression Normative Modelling and Transfer onto unseen site.
Expand All @@ -8,10 +8,15 @@ testing set, `see Saige’s
tutorial <https://github.com/predictive-clinical-neuroscience/PCNtoolkit-demo/blob/main/tutorials/ROI_blr_cortthick/NormativeModelTutorial.ipynb>`__
on Normative Modelling for more detail), the actual training of the
models, and will finally describe how to transfer the trained models
onto unseen sites.
onto unseen sites. The approach is described in detail in these papers:

- `Kia et al 2020 <https://arxiv.org/abs/2005.12055>`_.
- `Kia et al 2021 <https://www.biorxiv.org/content/10.1101/2021.05.28.446120v1.full>`_.

View on `GitHub <https://github.com/predictive-clinical-neuroscience/PCNtoolkit-demo>`_

While we run everything on a single compute node here, for larger datasets, it is probably desirbel to paralelize this using the normative_parallel functionality.

Run in `Google Colab <https://colab.research.google.com/github/predictive-clinical-neuroscience/PCNtoolkit-demo/blob/main/tutorials/HBR_FCON/HBR_NormativeModel_FCONdata_Tutorial.ipynb>`_


Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/genindex.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
4 changes: 2 additions & 2 deletions doc/build/html/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down Expand Up @@ -218,7 +218,7 @@ <h1>Predictive Clinical Neuroscience toolkit<a class="headerlink" href="#predict
<ul>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
</div>
<div class="toctree-wrapper compound">
Expand Down
Binary file modified doc/build/html/objects.inv
Binary file not shown.
2 changes: 1 addition & 1 deletion doc/build/html/pages/modindex.html
Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
17 changes: 11 additions & 6 deletions doc/build/html/pages/tutorial_HBR.html
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

<meta name="viewport" content="width=device-width, initial-scale=1.0" />

<title>Predictive Clinical Neuroscience Toolkit &mdash; Predictive Clinical Neuroscience Toolkit 0.20 documentation</title>
<title>Hierarchical Bayesian Regression &mdash; Predictive Clinical Neuroscience Toolkit 0.20 documentation</title>



Expand Down Expand Up @@ -111,7 +111,7 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Predictive Clinical Neuroscience Toolkit</a><ul>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Hierarchical Bayesian Regression</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#step-0-install-necessary-libraries-grab-data-files">Step 0: Install necessary libraries &amp; grab data files</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#overview">Overview</a></li>
</ul>
Expand Down Expand Up @@ -180,7 +180,7 @@

<li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>

<li>Predictive Clinical Neuroscience Toolkit</li>
<li>Hierarchical Bayesian Regression</li>


<li class="wy-breadcrumbs-aside">
Expand All @@ -199,16 +199,21 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<div class="section" id="predictive-clinical-neuroscience-toolkit">
<h1>Predictive Clinical Neuroscience Toolkit<a class="headerlink" href="#predictive-clinical-neuroscience-toolkit" title="Permalink to this headline"></a></h1>
<div class="section" id="hierarchical-bayesian-regression">
<h1>Hierarchical Bayesian Regression<a class="headerlink" href="#hierarchical-bayesian-regression" title="Permalink to this headline"></a></h1>
<p>Hierarchical Bayesian Regression Normative Modelling and Transfer onto unseen site.</p>
<p>This notebook will go through basic data preparation (training and
testing set, <a class="reference external" href="https://github.com/predictive-clinical-neuroscience/PCNtoolkit-demo/blob/main/tutorials/ROI_blr_cortthick/NormativeModelTutorial.ipynb">see Saige’s
tutorial</a>
on Normative Modelling for more detail), the actual training of the
models, and will finally describe how to transfer the trained models
onto unseen sites.</p>
onto unseen sites. The approach is described in detail in these papers:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://arxiv.org/abs/2005.12055">Kia et al 2020</a>.</p></li>
<li><p><a class="reference external" href="https://www.biorxiv.org/content/10.1101/2021.05.28.446120v1.full">Kia et al 2021</a>.</p></li>
</ul>
<p>View on <a class="reference external" href="https://github.com/predictive-clinical-neuroscience/PCNtoolkit-demo">GitHub</a></p>
<p>While we run everything on a single compute node here, for larger datasets, it is probably desirbel to paralelize this using the normative_parallel functionality.</p>
<p>Run in <a class="reference external" href="https://colab.research.google.com/github/predictive-clinical-neuroscience/PCNtoolkit-demo/blob/main/tutorials/HBR_FCON/HBR_NormativeModel_FCONdata_Tutorial.ipynb">Google Colab</a></p>
<p>Created by <a class="reference external" href="https://twitter.com/being_saige">Saige Rutherford</a>, adapted/edited by Andre Marquand and Pierre Berthet</p>
<div class="section" id="step-0-install-necessary-libraries-grab-data-files">
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/py-modindex.html
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/search.html
Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_CPC2020.html">Gaussian Process Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_ROIcorticalthickness.html">Bayesian Linear Regression</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Predictive Clinical Neuroscience Toolkit</a></li>
<li class="toctree-l1"><a class="reference internal" href="pages/tutorial_HBR.html">Hierarchical Bayesian Regression</a></li>
</ul>
<p class="caption"><span class="caption-text">Other Useful Stuff</span></p>
<ul>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/searchindex.js

Large diffs are not rendered by default.

0 comments on commit 89f5571

Please sign in to comment.