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ComputationalPsychiatry · Sep 27, 2023 · fa394ac · fa394ac
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diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/notebooks/0-Creating_networks.doctree b/.doctrees/notebooks/0-Creating_networks.doctree
diff --git a/.doctrees/notebooks/0-Theory.doctree b/.doctrees/notebooks/0-Theory.doctree
diff --git a/.doctrees/notebooks/1.1-Binary_HGF.doctree b/.doctrees/notebooks/1.1-Binary_HGF.doctree
diff --git a/.doctrees/notebooks/1.2-Categorical_HGF.doctree b/.doctrees/notebooks/1.2-Categorical_HGF.doctree
diff --git a/.doctrees/notebooks/1.3-Continuous_HGF.doctree b/.doctrees/notebooks/1.3-Continuous_HGF.doctree
diff --git a/.doctrees/notebooks/2-Using_custom_response_functions.doctree b/.doctrees/notebooks/2-Using_custom_response_functions.doctree
diff --git a/.doctrees/notebooks/3-Multilevel_HGF.doctree b/.doctrees/notebooks/3-Multilevel_HGF.doctree
diff --git a/.doctrees/notebooks/4-Parameter_recovery.doctree b/.doctrees/notebooks/4-Parameter_recovery.doctree
diff --git a/.doctrees/notebooks/Example_1_Heart_rate_variability.doctree b/.doctrees/notebooks/Example_1_Heart_rate_variability.doctree
diff --git a/.doctrees/notebooks/Exercise_1_Using_the_HGF.doctree b/.doctrees/notebooks/Exercise_1_Using_the_HGF.doctree
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diff --git a/notebooks/0-Creating_networks.html b/notebooks/0-Creating_networks.html
@@ -516,7 +516,7 @@ <h3>Visualizing probabilistic networks<a class="headerlink" href="#visualizing-p
 </div>
 <div class="cell_output docutils container">
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1695823931.436465    2225 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1695825755.704028    2374 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
 </pre></div>
 </div>
@@ -703,7 +703,7 @@ <h5>Continuous value coupling<a class="headerlink" href="#continuous-value-coupl
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/17ea0d0474a2df0370b32925eae9cac3bdc2904779562fdbda5e2d1ad65142d9.png" src="../_images/17ea0d0474a2df0370b32925eae9cac3bdc2904779562fdbda5e2d1ad65142d9.png" />
+<img alt="../_images/8bc9a77699f77a40aec50caf82b2ac0697c6b332e55dd342edff83a725da7f1f.png" src="../_images/8bc9a77699f77a40aec50caf82b2ac0697c6b332e55dd342edff83a725da7f1f.png" />
 </div>
 </div>
 <div class="admonition note">
@@ -786,7 +786,7 @@ <h5>Continuous volatility coupling<a class="headerlink" href="#continuous-volati
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/276240d6808dbf89cdb5942fc3e4e4d19ea19b139498bce2ed8a1e1c50508f02.png" src="../_images/276240d6808dbf89cdb5942fc3e4e4d19ea19b139498bce2ed8a1e1c50508f02.png" />
+<img alt="../_images/e6c0c03320d673aeb560953396cf8b1c0ac31f3f6f2da275c53cf96b9259171d.png" src="../_images/e6c0c03320d673aeb560953396cf8b1c0ac31f3f6f2da275c53cf96b9259171d.png" />
 </div>
 </div>
 <div class="admonition note">
@@ -879,7 +879,7 @@ <h5>Coupling with binary nodes<a class="headerlink" href="#coupling-with-binary-
 </div>
 </details>
 <div class="cell_output docutils container">
-<img alt="../_images/aa15055777f8e95de357c17fe882ebae009ca39bf1798b4fe5b717705dd22351.png" src="../_images/aa15055777f8e95de357c17fe882ebae009ca39bf1798b4fe5b717705dd22351.png" />
+<img alt="../_images/4564215c1306cd1d48d7dcbe2426b6cc347aaf29ee6156521371b62e91385b6f.png" src="../_images/4564215c1306cd1d48d7dcbe2426b6cc347aaf29ee6156521371b62e91385b6f.png" />
 </div>
 </div>
 <div class="admonition note">
@@ -974,8 +974,8 @@ <h1>System configuration<a class="headerlink" href="#system-configuration" title
 jax   : 0.4.16
 jaxlib: 0.4.16
 
-numpy     : 1.22.0
 seaborn   : 0.12.2
+numpy     : 1.22.0
 matplotlib: 3.8.0
 
 Watermark: 2.4.3

diff --git a/notebooks/0-Theory.html b/notebooks/0-Theory.html
@@ -975,9 +975,9 @@ <h1>System configuration<a class="headerlink" href="#system-configuration" title
 jax   : 0.4.16
 jaxlib: 0.4.16
 
-matplotlib: 3.8.0
 seaborn   : 0.12.2
 numpy     : 1.22.0
+matplotlib: 3.8.0
 
 Watermark: 2.4.3
 </pre></div>

diff --git a/notebooks/1.1-Binary_HGF.html b/notebooks/1.1-Binary_HGF.html
@@ -521,7 +521,7 @@ <h4>Create the model<a class="headerlink" href="#create-the-model" title="Permal
 </div>
 <div class="cell_output docutils container">
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1695823948.504619    2326 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1695825772.398742    2481 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
 </pre></div>
 </div>
@@ -731,7 +731,7 @@ <h4>Visualizing the model<a class="headerlink" href="#visualizing-the-model" tit
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/1a15384e5f028f47e4d386892b3055a6b0fcef2726014a94595bf012b0ff7162.svg" src="../_images/1a15384e5f028f47e4d386892b3055a6b0fcef2726014a94595bf012b0ff7162.svg" /></div>
+<img alt="../_images/0d547960d6c0cacb00155a6e657ec6784e1521e51a5fa0e376d8929e28e74702.svg" src="../_images/0d547960d6c0cacb00155a6e657ec6784e1521e51a5fa0e376d8929e28e74702.svg" /></div>
 </div>
 </section>
 <section id="sampling">
@@ -775,7 +775,7 @@ <h4>Sampling<a class="headerlink" href="#sampling" title="Permalink to this head
 </div><div class="output text_html">
     <div>
       <progress value='2000' class='' max='2000' style='width:300px; height:20px; vertical-align: middle;'></progress>
-      100.00% [2000/2000 00:04&lt;00:00 Sampling chain 0, 0 divergences]
+      100.00% [2000/2000 00:03&lt;00:00 Sampling chain 0, 0 divergences]
     </div>
     </div><div class="output text_html">
 <style>
@@ -798,7 +798,7 @@ <h4>Sampling<a class="headerlink" href="#sampling" title="Permalink to this head
       <progress value='2000' class='' max='2000' style='width:300px; height:20px; vertical-align: middle;'></progress>
       100.00% [2000/2000 00:02&lt;00:00 Sampling chain 1, 0 divergences]
     </div>
-    </div><div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 7 seconds.
+    </div><div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 6 seconds.
 </pre></div>
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -814,7 +814,7 @@ <h4>Sampling<a class="headerlink" href="#sampling" title="Permalink to this head
 </div>
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-<img alt="../_images/1f413ae20ae022313260c7a17fd149e92764df46ba53a1aab29ef4c4da5ffa2e.png" src="../_images/1f413ae20ae022313260c7a17fd149e92764df46ba53a1aab29ef4c4da5ffa2e.png" />
+<img alt="../_images/98926d0740456c4be18e72c9b0165efa97918bb9beb96af109dcca423a205925.png" src="../_images/98926d0740456c4be18e72c9b0165efa97918bb9beb96af109dcca423a205925.png" />
 </div>
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 </section>
@@ -863,7 +863,7 @@ <h3>Using the learned parameters<a class="headerlink" href="#using-the-learned-p
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-<img alt="../_images/cc442889e37030b9786120a0d2f267999aa942c8e3fab4799c4b08ec523fda34.png" src="../_images/cc442889e37030b9786120a0d2f267999aa942c8e3fab4799c4b08ec523fda34.png" />
+<img alt="../_images/b794f53fb00b8210017ec871a239d70f9a27be00b59702e8a289a72a702184f4.png" src="../_images/b794f53fb00b8210017ec871a239d70f9a27be00b59702e8a289a72a702184f4.png" />
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@@ -873,7 +873,7 @@ <h3>Using the learned parameters<a class="headerlink" href="#using-the-learned-p
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Array(202.52956, dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Array(202.52957, dtype=float32)
 </pre></div>
 </div>
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@@ -920,7 +920,7 @@ <h4>Visualizing the model<a class="headerlink" href="#id7" title="Permalink to t
 </div>
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-<img alt="../_images/3bfcdb1c8c20d77b0010d8b201cbc79873c153a68dd33301d3dc02c10761a048.svg" src="../_images/3bfcdb1c8c20d77b0010d8b201cbc79873c153a68dd33301d3dc02c10761a048.svg" /></div>
+<img alt="../_images/95ee7951fe67cfcede0a494dd6fbf41e0dd82e6d94572fdfd9760d8fa938b48e.svg" src="../_images/95ee7951fe67cfcede0a494dd6fbf41e0dd82e6d94572fdfd9760d8fa938b48e.svg" /></div>
 </div>
 </section>
 <section id="id8">
@@ -1003,7 +1003,7 @@ <h4>Sampling<a class="headerlink" href="#id8" title="Permalink to this heading">
 </div>
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-<img alt="../_images/e9084e8c1d54e795f7124b340adb394b8e9c7842b5c7f6200ee9a0d2d997580b.png" src="../_images/e9084e8c1d54e795f7124b340adb394b8e9c7842b5c7f6200ee9a0d2d997580b.png" />
+<img alt="../_images/c8a409938485a41600b05ce5ba1fc4ec479c3294d46da4714379af58e43f15f6.png" src="../_images/c8a409938485a41600b05ce5ba1fc4ec479c3294d46da4714379af58e43f15f6.png" />
 </div>
 </div>
 </section>
@@ -1053,7 +1053,7 @@ <h3>Using the learned parameters<a class="headerlink" href="#id9" title="Permali
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-<img alt="../_images/c30e1603c1a877edaf3c6bae0c883fb4ce2e3356672de25c86093d59eaf5a3b4.png" src="../_images/c30e1603c1a877edaf3c6bae0c883fb4ce2e3356672de25c86093d59eaf5a3b4.png" />
+<img alt="../_images/0530aae854af7e7e8bf7a866f3d3c0b528badb42a8b773f4dbc26db82ac65f59.png" src="../_images/0530aae854af7e7e8bf7a866f3d3c0b528badb42a8b773f4dbc26db82ac65f59.png" />
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@@ -1063,7 +1063,7 @@ <h3>Using the learned parameters<a class="headerlink" href="#id9" title="Permali
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Array(203.01332, dtype=float32)
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Array(203.01768, dtype=float32)
 </pre></div>
 </div>
 </div>
@@ -1092,11 +1092,11 @@ <h1>System configuration<a class="headerlink" href="#system-configuration" title
 jaxlib: 0.4.16
 
 matplotlib: 3.8.0
+sys       : 3.10.13 (main, Aug 28 2023, 08:28:42) [GCC 11.4.0]
 arviz     : 0.16.1
-pymc      : 5.8.2
 seaborn   : 0.12.2
-sys       : 3.10.13 (main, Aug 28 2023, 08:28:42) [GCC 11.4.0]
 jax       : 0.4.16
+pymc      : 5.8.2
 
 Watermark: 2.4.3
 </pre></div>

diff --git a/notebooks/1.2-Categorical_HGF.html b/notebooks/1.2-Categorical_HGF.html
@@ -518,7 +518,7 @@ <h2>Simulating a dataset<a class="headerlink" href="#simulating-a-dataset" title
 </div>
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-<img alt="../_images/bc0b2134fb181739f65b6f491e179bdf1d5a9b8e4dd6a2a678ef5741ff53b4f7.png" src="../_images/bc0b2134fb181739f65b6f491e179bdf1d5a9b8e4dd6a2a678ef5741ff53b4f7.png" />
+<img alt="../_images/864647b68718a786f6c0a305715ca0bfa0f9cf7b068eb4b9d25c494793e232ab.png" src="../_images/864647b68718a786f6c0a305715ca0bfa0f9cf7b068eb4b9d25c494793e232ab.png" />
 </div>
 </div>
 <div class="admonition note">
@@ -560,7 +560,7 @@ <h3>Creating the probabilistic network<a class="headerlink" href="#creating-the-
 </div>
 <div class="cell_output docutils container">
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1695824005.090974    2540 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1695825827.488250    2733 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
 </pre></div>
 </div>
@@ -648,7 +648,7 @@ <h3>Fitting the model forwards<a class="headerlink" href="#fitting-the-model-for
 </div>
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-<img alt="../_images/7d4e82bcaac1f799bf4758a53f7c8424be9d68fb3b7b6722a50f6666ad7c7a97.png" src="../_images/7d4e82bcaac1f799bf4758a53f7c8424be9d68fb3b7b6722a50f6666ad7c7a97.png" />
+<img alt="../_images/648c57d0c0987dd1202130639a8d13ec0b0892dfffcc332786b421b1d19dc607.png" src="../_images/648c57d0c0987dd1202130639a8d13ec0b0892dfffcc332786b421b1d19dc607.png" />
 </div>
 </details>
 </div>
@@ -798,12 +798,12 @@ <h1>System configuration<a class="headerlink" href="#system-configuration" title
 jax   : 0.4.16
 jaxlib: 0.4.16
 
-sys       : 3.10.13 (main, Aug 28 2023, 08:28:42) [GCC 11.4.0]
-seaborn   : 0.12.2
 jax       : 0.4.16
-matplotlib: 3.8.0
+seaborn   : 0.12.2
 numpy     : 1.22.0
 pytensor  : 2.16.3
+matplotlib: 3.8.0
+sys       : 3.10.13 (main, Aug 28 2023, 08:28:42) [GCC 11.4.0]
 
 Watermark: 2.4.3
 </pre></div>