Deploying to gh-pages from @ 2c6a546 🚀

ComputationalPsychiatry · Jun 25, 2024 · 627ca3a · 627ca3a
1 parent 411d626
commit 627ca3a
Show file tree

Hide file tree

Showing 142 changed files with 239 additions and 1,032 deletions.
diff --git a/dev/.doctrees/api.doctree b/dev/.doctrees/api.doctree
diff --git a/dev/.doctrees/environment.pickle b/dev/.doctrees/environment.pickle
diff --git a/dev/.doctrees/generated/pyhgf.utils/pyhgf.utils.trim_sequence.doctree b/dev/.doctrees/generated/pyhgf.utils/pyhgf.utils.trim_sequence.doctree
diff --git a/dev/.doctrees/notebooks/0.1-Theory.doctree b/dev/.doctrees/notebooks/0.1-Theory.doctree
diff --git a/dev/.doctrees/notebooks/0.2-Creating_networks.doctree b/dev/.doctrees/notebooks/0.2-Creating_networks.doctree
diff --git a/dev/.doctrees/notebooks/0.3-Generalised_filtering.doctree b/dev/.doctrees/notebooks/0.3-Generalised_filtering.doctree
diff --git a/dev/.doctrees/notebooks/1.1-Binary_HGF.doctree b/dev/.doctrees/notebooks/1.1-Binary_HGF.doctree
diff --git a/dev/.doctrees/notebooks/1.2-Categorical_HGF.doctree b/dev/.doctrees/notebooks/1.2-Categorical_HGF.doctree
diff --git a/dev/.doctrees/notebooks/1.3-Continuous_HGF.doctree b/dev/.doctrees/notebooks/1.3-Continuous_HGF.doctree
diff --git a/dev/.doctrees/notebooks/2-Using_custom_response_functions.doctree b/dev/.doctrees/notebooks/2-Using_custom_response_functions.doctree
diff --git a/dev/.doctrees/notebooks/3-Multilevel_HGF.doctree b/dev/.doctrees/notebooks/3-Multilevel_HGF.doctree
diff --git a/dev/.doctrees/notebooks/4-Parameter_recovery.doctree b/dev/.doctrees/notebooks/4-Parameter_recovery.doctree
diff --git a/dev/.doctrees/notebooks/Example_1_Heart_rate_variability.doctree b/dev/.doctrees/notebooks/Example_1_Heart_rate_variability.doctree
diff --git a/dev/.doctrees/notebooks/Example_2_Input_node_volatility_coupling.doctree b/dev/.doctrees/notebooks/Example_2_Input_node_volatility_coupling.doctree
diff --git a/dev/.doctrees/notebooks/Example_3_Multi_armed_bandit.doctree b/dev/.doctrees/notebooks/Example_3_Multi_armed_bandit.doctree
diff --git a/dev/.doctrees/notebooks/Exercise_1_Using_the_HGF.doctree b/dev/.doctrees/notebooks/Exercise_1_Using_the_HGF.doctree
diff --git a/dev/_images/069d1ee05d4ff0f25cf5a254f45c228fee0f065679f69bca17966e8e31338ac9.png b/dev/_images/069d1ee05d4ff0f25cf5a254f45c228fee0f065679f69bca17966e8e31338ac9.png
diff --git a/dev/_images/0dd78da6e2665d40e3bee7729ad1c7356d888cf18741878c146b4e2977e57f1d.png b/dev/_images/0dd78da6e2665d40e3bee7729ad1c7356d888cf18741878c146b4e2977e57f1d.png
diff --git a/dev/_images/1a9c6386c0750b59cbe40f05e92535412c4ca5bdde608f1cc4d998af6a706d59.png b/dev/_images/1a9c6386c0750b59cbe40f05e92535412c4ca5bdde608f1cc4d998af6a706d59.png
diff --git a/...d7adb40e86a06d3c587c73103c1d2a5698bb6.svg → ...69ac0c4a8b7994776641b7ca80207aba0e073.svg b/...d7adb40e86a06d3c587c73103c1d2a5698bb6.svg → ...69ac0c4a8b7994776641b7ca80207aba0e073.svg
diff --git a/...90c832e9b204e89fed0d0688e3e2fdb1677dd.svg → ...ab3600af54719c813af4a3f819412cb3c0342.svg b/...90c832e9b204e89fed0d0688e3e2fdb1677dd.svg → ...ab3600af54719c813af4a3f819412cb3c0342.svg
diff --git a/dev/_images/3196790868bd68409526f9b44b04f37b5ef45d1ac49b25709797b8f4f963da2e.png b/dev/_images/3196790868bd68409526f9b44b04f37b5ef45d1ac49b25709797b8f4f963da2e.png
diff --git a/dev/_images/35bd8e7a64b760abcea9afbdc164b50c5aad01ba5742b665bbccf2c46cff4954.png b/dev/_images/35bd8e7a64b760abcea9afbdc164b50c5aad01ba5742b665bbccf2c46cff4954.png
diff --git a/dev/_images/36155f98f2f42014555b30735279260feb84cba339f7d5c083b876a4cf2ad7f4.png b/dev/_images/36155f98f2f42014555b30735279260feb84cba339f7d5c083b876a4cf2ad7f4.png
diff --git a/dev/_images/3d0e1e2975a5e07ba48ce05cdd20179c7de0eb330aa2018678ee872916c09ee6.png b/dev/_images/3d0e1e2975a5e07ba48ce05cdd20179c7de0eb330aa2018678ee872916c09ee6.png
diff --git a/dev/_images/3ef1858c1f4053acda5996876a4d4c39795bef53215ec95256d9401080f6c90c.png b/dev/_images/3ef1858c1f4053acda5996876a4d4c39795bef53215ec95256d9401080f6c90c.png
diff --git a/dev/_images/4a29fa1c347597ac1b751ae5fb338df7bead0f2a2508cf3ecc1ccf11b09dd930.png b/dev/_images/4a29fa1c347597ac1b751ae5fb338df7bead0f2a2508cf3ecc1ccf11b09dd930.png
diff --git a/dev/_images/4f5c182796491f195a4627f87aac27b055fa37e4d4822b0176b7bd3faaa26a5d.png b/dev/_images/4f5c182796491f195a4627f87aac27b055fa37e4d4822b0176b7bd3faaa26a5d.png
diff --git a/dev/_images/51209b59e0ea1cd2c3d6cf8e9ea8a4c4951d5f665af0527085d9fccfe0629386.png b/dev/_images/51209b59e0ea1cd2c3d6cf8e9ea8a4c4951d5f665af0527085d9fccfe0629386.png
diff --git a/dev/_images/5695d602120e9ce125e6485b39960dda87af0667e36965a8e897bd7540ab14f8.png b/dev/_images/5695d602120e9ce125e6485b39960dda87af0667e36965a8e897bd7540ab14f8.png
diff --git a/dev/_images/5772b9033c601b7591c6b779ccd2cbffdd3474082870bc679c28801d98e4c3e2.png b/dev/_images/5772b9033c601b7591c6b779ccd2cbffdd3474082870bc679c28801d98e4c3e2.png
diff --git a/dev/_images/5b40a8a820438d3a653d42daa3586f168b2c6bfed46475ee03de375589cff068.png b/dev/_images/5b40a8a820438d3a653d42daa3586f168b2c6bfed46475ee03de375589cff068.png
diff --git a/dev/_images/60aa1d4a9b36fe978140d9391b1e995e53e9e1f049a6152ee267c80b2d34da59.png b/dev/_images/60aa1d4a9b36fe978140d9391b1e995e53e9e1f049a6152ee267c80b2d34da59.png
diff --git a/dev/_images/61c7e232230a91651cfc6b6408a19946ecd55642472caad03b4541635a070ca3.png b/dev/_images/61c7e232230a91651cfc6b6408a19946ecd55642472caad03b4541635a070ca3.png
diff --git a/dev/_images/62a2318a6a862a397e546b65bba8584576bd3cd17d8c6b934d326bdee85c2225.png b/dev/_images/62a2318a6a862a397e546b65bba8584576bd3cd17d8c6b934d326bdee85c2225.png
diff --git a/dev/_images/678d72a60295d97880730630c83c73f67df65c6f6f3947670953cc116558cd8f.png b/dev/_images/678d72a60295d97880730630c83c73f67df65c6f6f3947670953cc116558cd8f.png
diff --git a/dev/_images/67b1040bc053826c3ed1ca2a0ac759b2f2ea2b7216fe42cced6ce07ca3f0d664.png b/dev/_images/67b1040bc053826c3ed1ca2a0ac759b2f2ea2b7216fe42cced6ce07ca3f0d664.png
diff --git a/dev/_images/67e2f2943271cf56e415b086ddc6b5ae659e86dc527c9c89f611fd50f96c06c3.png b/dev/_images/67e2f2943271cf56e415b086ddc6b5ae659e86dc527c9c89f611fd50f96c06c3.png
diff --git a/dev/_images/6a4465485a496aa61e16d53dcbc9bcdcc555887e76683a1228023adb8db8ddc5.png b/dev/_images/6a4465485a496aa61e16d53dcbc9bcdcc555887e76683a1228023adb8db8ddc5.png
diff --git a/dev/_images/6ee736a433496109927a5d41c92e6986147148fc51ee235d8a2770c7466966a9.png b/dev/_images/6ee736a433496109927a5d41c92e6986147148fc51ee235d8a2770c7466966a9.png
diff --git a/dev/_images/6f6d53d44dd3fe60e09f81befd10ca7b58ae234ae00e7a93743172ab67280a4b.png b/dev/_images/6f6d53d44dd3fe60e09f81befd10ca7b58ae234ae00e7a93743172ab67280a4b.png
diff --git a/dev/_images/706404259364564618aad7b43903873c0e3d15fe90f24af1c84ed5c109c14938.png b/dev/_images/706404259364564618aad7b43903873c0e3d15fe90f24af1c84ed5c109c14938.png
diff --git a/dev/_images/712296b972e372b760a5ec86c8f9bc9a8bd1c6f1e9fb2e1968d61923f5aa3442.png b/dev/_images/712296b972e372b760a5ec86c8f9bc9a8bd1c6f1e9fb2e1968d61923f5aa3442.png
diff --git a/dev/_images/7197ef2f3e799a782682698b69b70498c111ccf647512ea0f85b79361f02c75c.png b/dev/_images/7197ef2f3e799a782682698b69b70498c111ccf647512ea0f85b79361f02c75c.png
diff --git a/dev/_images/736587a3b7f65798cfa0565aa29fbb953015b3a50b4f78a34729a0a3a738486d.png b/dev/_images/736587a3b7f65798cfa0565aa29fbb953015b3a50b4f78a34729a0a3a738486d.png
diff --git a/dev/_images/751c7b9603154fae23b8d75665e816272ed5202d87953dc975a6e0faed225885.png b/dev/_images/751c7b9603154fae23b8d75665e816272ed5202d87953dc975a6e0faed225885.png
diff --git a/dev/_images/7985af4975b580f5122a3135b37e4a866172504ae3122f14b2025d93eda48680.png b/dev/_images/7985af4975b580f5122a3135b37e4a866172504ae3122f14b2025d93eda48680.png
diff --git a/dev/_images/7d4a59ed45e353ff111445cb52a5add716f1a12b8f56ebe94081f2786f6ee1f1.png b/dev/_images/7d4a59ed45e353ff111445cb52a5add716f1a12b8f56ebe94081f2786f6ee1f1.png
diff --git a/dev/_images/8132b0604342f9310a4fea36bb5024ee13c323d66b932378f810b43488e26e4a.png b/dev/_images/8132b0604342f9310a4fea36bb5024ee13c323d66b932378f810b43488e26e4a.png
diff --git a/dev/_images/83acf72d3d3dd58f16ad84a6c0ef2fc2fdcd902cb174e0877ae8ae446d21704f.png b/dev/_images/83acf72d3d3dd58f16ad84a6c0ef2fc2fdcd902cb174e0877ae8ae446d21704f.png
diff --git a/dev/_images/8810d5a96d575f5eb71a284d8c22102e3ff4c486c464577b5ef68272ed28b45e.png b/dev/_images/8810d5a96d575f5eb71a284d8c22102e3ff4c486c464577b5ef68272ed28b45e.png
diff --git a/...d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg → ...2d75a89a86b3ef90438ded772ac7bf43de688.svg b/...d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg → ...2d75a89a86b3ef90438ded772ac7bf43de688.svg
diff --git a/dev/_images/964d9b61ebfd05982932507a8b81a117995998a800eb75a96af7d4999d5fd63e.png b/dev/_images/964d9b61ebfd05982932507a8b81a117995998a800eb75a96af7d4999d5fd63e.png
diff --git a/...736e4d37dff09815109de1a6e7fa6aef919ab.svg → ...593b4cbb06da4a6936da0f16fc8c9c2b9a045.svg b/...736e4d37dff09815109de1a6e7fa6aef919ab.svg → ...593b4cbb06da4a6936da0f16fc8c9c2b9a045.svg
diff --git a/dev/_images/a26cdac4932469d021ed9132a57310b7bb44bbd99ec2338e61a7dcc77e1e5fe0.png b/dev/_images/a26cdac4932469d021ed9132a57310b7bb44bbd99ec2338e61a7dcc77e1e5fe0.png
diff --git a/dev/_images/b7486985f96a5316e408c9652d8f487f8dee766d59ec97283428f14bd4f84556.png b/dev/_images/b7486985f96a5316e408c9652d8f487f8dee766d59ec97283428f14bd4f84556.png
diff --git a/dev/_images/b8073ea7f3bd29b22a6e7ba214545ee30692d808f390c63d0855ccc8573b925a.png b/dev/_images/b8073ea7f3bd29b22a6e7ba214545ee30692d808f390c63d0855ccc8573b925a.png
diff --git a/dev/_images/baa286783abe83438a4794a8dcd4cf4f22071b702e4d891d4e2296e5a3cecee9.png b/dev/_images/baa286783abe83438a4794a8dcd4cf4f22071b702e4d891d4e2296e5a3cecee9.png
diff --git a/dev/_images/bd946bbca2a8ac21b55e610e374cede57403974d59d889ba3aad74df5c73da0a.png b/dev/_images/bd946bbca2a8ac21b55e610e374cede57403974d59d889ba3aad74df5c73da0a.png
diff --git a/dev/_images/c2d45789840f7282b1e4e2003c9286a6ec07e10896c60df3a26eed890d07f72b.png b/dev/_images/c2d45789840f7282b1e4e2003c9286a6ec07e10896c60df3a26eed890d07f72b.png
diff --git a/dev/_images/c7143159a6ea403937554b62024f08398aae8bfe1c00a32353a406a6555be390.png b/dev/_images/c7143159a6ea403937554b62024f08398aae8bfe1c00a32353a406a6555be390.png
diff --git a/dev/_images/d9f8912ee6f3583094cbbfc29c1254899764be1388478fed5a876c40ca8c84ee.png b/dev/_images/d9f8912ee6f3583094cbbfc29c1254899764be1388478fed5a876c40ca8c84ee.png
diff --git a/dev/_images/deb2c1914fe72bc398506b376d1eeafda5089f131df30d0c9964a615164f37fd.png b/dev/_images/deb2c1914fe72bc398506b376d1eeafda5089f131df30d0c9964a615164f37fd.png
diff --git a/dev/_images/e3680cee924b12435d2440c9912a54ea01c24f76306a0bcf628e55b34076a918.png b/dev/_images/e3680cee924b12435d2440c9912a54ea01c24f76306a0bcf628e55b34076a918.png
diff --git a/dev/_images/e916463221ed5b920e4afcc1c8adeebd9f3b938e92ea87df3e188215e5a081dc.png b/dev/_images/e916463221ed5b920e4afcc1c8adeebd9f3b938e92ea87df3e188215e5a081dc.png
diff --git a/dev/_images/fdb1c763c9d74be824cb679d1619022ffb7396b46e7db24535140a8ce4e49722.png b/dev/_images/fdb1c763c9d74be824cb679d1619022ffb7396b46e7db24535140a8ce4e49722.png
diff --git a/dev/_modules/pyhgf/math.html b/dev/_modules/pyhgf/math.html
@@ -751,6 +751,11 @@ <h1>Source code for pyhgf.math</h1><div class="highlight"><pre>
         <span class="o">+</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">expected_mean</span><span class="p">)</span> <span class="o">*</span> <span class="n">gaussian_density</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">eta0</span><span class="p">,</span> <span class="n">expected_precision</span><span class="p">)</span>
     <span class="p">)</span></div>
 
+
+
+<span class="k">def</span> <span class="nf">sigmoid_inverse_temperature</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">temperature</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Compute the sigmoid response function with inverse temperature parameter.&quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="p">(</span><span class="n">x</span><span class="o">**</span><span class="n">temperature</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">x</span><span class="o">**</span><span class="n">temperature</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">x</span><span class="p">)</span> <span class="o">**</span> <span class="n">temperature</span><span class="p">)</span>
 </pre></div>
 
                 </article>

diff --git a/dev/_modules/pyhgf/utils.html b/dev/_modules/pyhgf/utils.html
@@ -561,42 +561,6 @@ <h1>Source code for pyhgf.utils</h1><div class="highlight"><pre>
 
 
 
-<div class="viewcode-block" id="trim_sequence">
-<a class="viewcode-back" href="../../generated/pyhgf.utils/pyhgf.utils.trim_sequence.html#pyhgf.utils.trim_sequence">[docs]</a>
-<span class="k">def</span> <span class="nf">trim_sequence</span><span class="p">(</span>
-    <span class="n">exclude_node_idxs</span><span class="p">:</span> <span class="n">List</span><span class="p">,</span> <span class="n">update_sequence</span><span class="p">:</span> <span class="n">UpdateSequence</span><span class="p">,</span> <span class="n">edges</span><span class="p">:</span> <span class="n">Tuple</span>
-<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">UpdateSequence</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Remove steps from an update sequence that depends on a set of nodes.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    exclude_node_idxs :</span>
-<span class="sd">        A list of node indexes. The nodes can be input nodes or any other node in the</span>
-<span class="sd">        network.</span>
-<span class="sd">    update_sequence :</span>
-<span class="sd">        The sequence of updates that will be applied to the node structure.</span>
-<span class="sd">    edges :</span>
-<span class="sd">        The nodes structure.</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">    -------</span>
-<span class="sd">    trimmed_update_sequence :</span>
-<span class="sd">        The update sequence without the update steps for nodes depending on the root</span>
-<span class="sd">        list.</span>
-
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># list the nodes that depend on the root indexes</span>
-    <span class="n">branch_list</span> <span class="o">=</span> <span class="n">list_branches</span><span class="p">(</span><span class="n">node_idxs</span><span class="o">=</span><span class="n">exclude_node_idxs</span><span class="p">,</span> <span class="n">edges</span><span class="o">=</span><span class="n">edges</span><span class="p">)</span>
-
-    <span class="c1"># remove the update steps that are targetting the excluded nodes</span>
-    <span class="n">trimmed_update_sequence</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
-        <span class="p">[</span><span class="n">seq</span> <span class="k">for</span> <span class="n">seq</span> <span class="ow">in</span> <span class="n">update_sequence</span> <span class="k">if</span> <span class="n">seq</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">branch_list</span><span class="p">]</span>
-    <span class="p">)</span>
-
-    <span class="k">return</span> <span class="n">trimmed_update_sequence</span></div>
-
-
-
 <div class="viewcode-block" id="list_branches">
 <a class="viewcode-back" href="../../generated/pyhgf.utils/pyhgf.utils.list_branches.html#pyhgf.utils.list_branches">[docs]</a>
 <span class="k">def</span> <span class="nf">list_branches</span><span class="p">(</span><span class="n">node_idxs</span><span class="p">:</span> <span class="n">List</span><span class="p">,</span> <span class="n">edges</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">branch_list</span><span class="p">:</span> <span class="n">List</span> <span class="o">=</span> <span class="p">[])</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">:</span>

diff --git a/dev/_sources/generated/pyhgf.utils/pyhgf.utils.trim_sequence.rst.txt b/dev/_sources/generated/pyhgf.utils/pyhgf.utils.trim_sequence.rst.txt