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a/_images/8e13d3fa71ea9b734811483035e21406ecf61b532e57f8699aebe920d35e0fb9.png b/_images/8e13d3fa71ea9b734811483035e21406ecf61b532e57f8699aebe920d35e0fb9.png deleted file mode 100644 index 19b0ac7b9..000000000 Binary files a/_images/8e13d3fa71ea9b734811483035e21406ecf61b532e57f8699aebe920d35e0fb9.png and /dev/null differ diff --git a/_images/8fc9c210ab62f5dd9a3be3ce533d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg b/_images/8f02834ccc45a1fbb4bd4aabfac2d75a89a86b3ef90438ded772ac7bf43de688.svg similarity index 100% rename from _images/8fc9c210ab62f5dd9a3be3ce533d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg rename to _images/8f02834ccc45a1fbb4bd4aabfac2d75a89a86b3ef90438ded772ac7bf43de688.svg index a85f1c417..0255e9b57 100644 --- a/_images/8fc9c210ab62f5dd9a3be3ce533d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg +++ b/_images/8f02834ccc45a1fbb4bd4aabfac2d75a89a86b3ef90438ded772ac7bf43de688.svg @@ -9,22 +9,22 @@ %3 - - -tonic_volatility_2 - -tonic_volatility_2 -~ -Normal - - + hgf_loglike hgf_loglike ~ Potential + + +tonic_volatility_2 + +tonic_volatility_2 +~ +Normal + tonic_volatility_2->hgf_loglike diff --git a/_images/69539e2739458d7218e514133841304a4e4b0eb711fc8054497123f2e226d095.svg b/_images/906f003ac3c62510821da40b51513f921c716a616f423184ce543353e719929c.svg similarity index 100% rename from _images/69539e2739458d7218e514133841304a4e4b0eb711fc8054497123f2e226d095.svg rename to _images/906f003ac3c62510821da40b51513f921c716a616f423184ce543353e719929c.svg index 02b4163cb..3357dc509 100644 --- a/_images/69539e2739458d7218e514133841304a4e4b0eb711fc8054497123f2e226d095.svg +++ b/_images/906f003ac3c62510821da40b51513f921c716a616f423184ce543353e719929c.svg @@ -9,22 +9,22 @@ %3 - - -hgf_loglike - -hgf_loglike -~ -Potential - - + tonic_volatility_3 tonic_volatility_3 ~ Normal + + +hgf_loglike + +hgf_loglike +~ +Potential + tonic_volatility_3->hgf_loglike diff --git a/_images/912fffdcd2054c64eed5d2aa8bf4727c5e1de8d1da7009137538546b84545cba.png b/_images/912fffdcd2054c64eed5d2aa8bf4727c5e1de8d1da7009137538546b84545cba.png new file mode 100644 index 000000000..b7cc0de59 Binary files /dev/null and b/_images/912fffdcd2054c64eed5d2aa8bf4727c5e1de8d1da7009137538546b84545cba.png differ diff --git a/_images/961af07fc8eca6d3dc1184d57c097db7ad086431fc2972c9a6c3aa606e2fcc19.png b/_images/961af07fc8eca6d3dc1184d57c097db7ad086431fc2972c9a6c3aa606e2fcc19.png new file mode 100644 index 000000000..e7ca65c17 Binary files /dev/null and b/_images/961af07fc8eca6d3dc1184d57c097db7ad086431fc2972c9a6c3aa606e2fcc19.png differ diff --git a/_images/99baaf96994441c801b09e398badaa2fec3fa62b5da6d4541c28b2374857cc78.png b/_images/99baaf96994441c801b09e398badaa2fec3fa62b5da6d4541c28b2374857cc78.png deleted file mode 100644 index 1f7bf6935..000000000 Binary files a/_images/99baaf96994441c801b09e398badaa2fec3fa62b5da6d4541c28b2374857cc78.png and /dev/null differ diff --git a/_images/9dd169223f849709d0e96f9e2b359b7e54bb489c486433223b1de934ec60675d.png 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a/_images/fc9c9d0ad7db3f8618a8fab2954880ab258dbe4672cdeda6d28e830f0e0fb36a.png b/_images/fc9c9d0ad7db3f8618a8fab2954880ab258dbe4672cdeda6d28e830f0e0fb36a.png new file mode 100644 index 000000000..2b04dc843 Binary files /dev/null and b/_images/fc9c9d0ad7db3f8618a8fab2954880ab258dbe4672cdeda6d28e830f0e0fb36a.png differ diff --git a/_modules/index.html b/_modules/index.html index 7a1223c4e..fd45e3fa8 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -438,7 +438,6 @@

All modules for which code is available

diff --git a/_modules/pyhgf/networks.html b/_modules/pyhgf/utils.html similarity index 98% rename from _modules/pyhgf/networks.html rename to _modules/pyhgf/utils.html index 3248b25d8..203f1a8d8 100644 --- a/_modules/pyhgf/networks.html +++ b/_modules/pyhgf/utils.html @@ -7,7 +7,7 @@ - pyhgf.networks — pyhgf 0.0.18 documentation + pyhgf.utils — pyhgf 0.0.18 documentation @@ -48,7 +48,7 @@ - + @@ -420,7 +420,7 @@
  • Module code
    • -
  • pyhgf.networks
    • +
  • pyhgf.utils
    • @@ -437,7 +437,7 @@
    -

    Source code for pyhgf.networks

    +  
    Source code for pyhgf.utils
     # Author: Nicolas Legrand <nicolas.legrand@cas.au.dk>
 
 from functools import partial
@@ -477,7 +477,7 @@ 
    Source code for pyhgf.networks
     
 
 
    
-[docs]
+[docs]
 @partial(jit, static_argnames=("update_sequence", "structure"))
 def beliefs_propagation(
     attributes: Attributes,
@@ -551,7 +551,7 @@ 
    Source code for pyhgf.networks
     
 
 
    
-[docs]
+[docs]
 def trim_sequence(
     exclude_node_idxs: List, update_sequence: UpdateSequence, edges: Tuple
 ) -> UpdateSequence:
@@ -587,7 +587,7 @@ 
    Source code for pyhgf.networks
     
 
 
    
-[docs]
+[docs]
 def list_branches(node_idxs: List, edges: Tuple, branch_list: List = []) -> List:
     """Return the branch of a network from a given set of root nodes.
 
@@ -647,7 +647,7 @@ 
    Source code for pyhgf.networks
     
 
 
    
-[docs]
+[docs]
 def fill_categorical_state_node(
     network: "Network",
     node_idx: int,
@@ -730,7 +730,7 @@ 
    Source code for pyhgf.networks
     
 
 
    
-[docs]
+[docs]
 def get_update_sequence(network: "Network", update_type: str) -> List:
     """Generate an update sequence from the network's structure.
 
diff --git a/_sources/api.rst.txt b/_sources/api.rst.txt
index c09fddf83..8802acd68 100644
--- a/_sources/api.rst.txt
+++ b/_sources/api.rst.txt
@@ -203,15 +203,15 @@ least the HGF instance as input after observation and returning surprise.
    binary_softmax
    binary_softmax_inverse_temperature
 
-Networks
-********
+Utils
+*****
 
-Utilities for manipulating networks of probabilistic nodes.
+Utilities for manipulating neural networks.
 
-.. currentmodule:: pyhgf.networks
+.. currentmodule:: pyhgf.utils
 
 .. autosummary::
-   :toctree: generated/pyhgf.networks
+   :toctree: generated/pyhgf.utils
 
    beliefs_propagation
    trim_sequence
diff --git a/_sources/generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.rst.txt b/_sources/generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.rst.txt
deleted file mode 100644
index cb2ecbd36..000000000
--- a/_sources/generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.rst.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyhgf.networks.beliefs\_propagation
-===================================
-
-.. currentmodule:: pyhgf.networks
-
-.. autofunction:: beliefs_propagation
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.rst.txt b/_sources/generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.rst.txt
deleted file mode 100644
index c5147f3ca..000000000
--- a/_sources/generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.rst.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyhgf.networks.fill\_categorical\_state\_node
-=============================================
-
-.. currentmodule:: pyhgf.networks
-
-.. autofunction:: fill_categorical_state_node
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.networks/pyhgf.networks.get_update_sequence.rst.txt b/_sources/generated/pyhgf.networks/pyhgf.networks.get_update_sequence.rst.txt
deleted file mode 100644
index 2f43b4ee2..000000000
--- a/_sources/generated/pyhgf.networks/pyhgf.networks.get_update_sequence.rst.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyhgf.networks.get\_update\_sequence
-====================================
-
-.. currentmodule:: pyhgf.networks
-
-.. autofunction:: get_update_sequence
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.networks/pyhgf.networks.list_branches.rst.txt b/_sources/generated/pyhgf.networks/pyhgf.networks.list_branches.rst.txt
deleted file mode 100644
index c25afbd3b..000000000
--- a/_sources/generated/pyhgf.networks/pyhgf.networks.list_branches.rst.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyhgf.networks.list\_branches
-=============================
-
-.. currentmodule:: pyhgf.networks
-
-.. autofunction:: list_branches
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.networks/pyhgf.networks.trim_sequence.rst.txt b/_sources/generated/pyhgf.networks/pyhgf.networks.trim_sequence.rst.txt
deleted file mode 100644
index 3bd08cd12..000000000
--- a/_sources/generated/pyhgf.networks/pyhgf.networks.trim_sequence.rst.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyhgf.networks.trim\_sequence
-=============================
-
-.. currentmodule:: pyhgf.networks
-
-.. autofunction:: trim_sequence
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.rst.txt b/_sources/generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.rst.txt
new file mode 100644
index 000000000..494978e3f
--- /dev/null
+++ b/_sources/generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.rst.txt
@@ -0,0 +1,6 @@
+pyhgf.utils.beliefs\_propagation
+================================
+
+.. currentmodule:: pyhgf.utils
+
+.. autofunction:: beliefs_propagation
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.rst.txt b/_sources/generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.rst.txt
new file mode 100644
index 000000000..81450f4bf
--- /dev/null
+++ b/_sources/generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.rst.txt
@@ -0,0 +1,6 @@
+pyhgf.utils.fill\_categorical\_state\_node
+==========================================
+
+.. currentmodule:: pyhgf.utils
+
+.. autofunction:: fill_categorical_state_node
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.utils/pyhgf.utils.get_update_sequence.rst.txt b/_sources/generated/pyhgf.utils/pyhgf.utils.get_update_sequence.rst.txt
new file mode 100644
index 000000000..bbe8607ae
--- /dev/null
+++ b/_sources/generated/pyhgf.utils/pyhgf.utils.get_update_sequence.rst.txt
@@ -0,0 +1,6 @@
+pyhgf.utils.get\_update\_sequence
+=================================
+
+.. currentmodule:: pyhgf.utils
+
+.. autofunction:: get_update_sequence
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.utils/pyhgf.utils.list_branches.rst.txt b/_sources/generated/pyhgf.utils/pyhgf.utils.list_branches.rst.txt
new file mode 100644
index 000000000..65a4d1c60
--- /dev/null
+++ b/_sources/generated/pyhgf.utils/pyhgf.utils.list_branches.rst.txt
@@ -0,0 +1,6 @@
+pyhgf.utils.list\_branches
+==========================
+
+.. currentmodule:: pyhgf.utils
+
+.. autofunction:: list_branches
\ No newline at end of file
diff --git a/_sources/generated/pyhgf.utils/pyhgf.utils.trim_sequence.rst.txt b/_sources/generated/pyhgf.utils/pyhgf.utils.trim_sequence.rst.txt
new file mode 100644
index 000000000..da88dd6e2
--- /dev/null
+++ b/_sources/generated/pyhgf.utils/pyhgf.utils.trim_sequence.rst.txt
@@ -0,0 +1,6 @@
+pyhgf.utils.trim\_sequence
+==========================
+
+.. currentmodule:: pyhgf.utils
+
+.. autofunction:: trim_sequence
\ No newline at end of file
diff --git a/_sources/notebooks/0.3-Generalised_filtering.ipynb.txt b/_sources/notebooks/0.3-Generalised_filtering.ipynb.txt
index 3ae750155..edc1a9f73 100644
--- a/_sources/notebooks/0.3-Generalised_filtering.ipynb.txt
+++ b/_sources/notebooks/0.3-Generalised_filtering.ipynb.txt
@@ -38,7 +38,7 @@
     "from matplotlib.ticker import MultipleLocator\n",
     "from pyhgf.math import MultivariateNormal, Normal, gaussian_predictive_distribution\n",
     "from pyhgf.model import HGF\n",
-    "from pyhgf.networks import beliefs_propagation\n",
+    "from pyhgf.utils import beliefs_propagation\n",
     "from scipy.special import gammaln\n",
     "from scipy.stats import norm, t\n",
     "\n",
diff --git a/_sources/notebooks/Example_3_Multi_armed_bandit.ipynb.txt b/_sources/notebooks/Example_3_Multi_armed_bandit.ipynb.txt
index a63967026..1317b2413 100644
--- a/_sources/notebooks/Example_3_Multi_armed_bandit.ipynb.txt
+++ b/_sources/notebooks/Example_3_Multi_armed_bandit.ipynb.txt
@@ -942,7 +942,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyhgf.networks import beliefs_propagation"
+    "from pyhgf.utils import beliefs_propagation"
    ]
   },
   {
diff --git a/api.html b/api.html
index 5ab3b0bc5..f3242540c 100644
--- a/api.html
+++ b/api.html
@@ -483,7 +483,7 @@
 
  • Model
    • 
 
  • Plots
    • 
 
  • Response
    • 
-
  • Networks
    • 
+
  • Utils
    • 
 
  • Math
    • 
 
 
@@ -713,24 +713,24 @@ 
    Response
 
 
-
    
-
    Networks#
    
-
    Utilities for manipulating networks of probabilistic nodes.
    
+
    
+
    Utils#
    
+
    Utilities for manipulating neural networks.
    
 
-
+
-
+
-
+
-
+
-
+
@@ -850,7 +850,7 @@ 
    MathModel
 
  • Plots
    • 
 
  • Response
    • 
-
  • Networks
    • 
+
  • Utils
    • 
 
  • Math
    • 
 
   
diff --git a/generated/pyhgf.distribution/pyhgf.distribution.HGFDistribution.html b/generated/pyhgf.distribution/pyhgf.distribution.HGFDistribution.html
index 0f8e2de9e..de508059e 100644
--- a/generated/pyhgf.distribution/pyhgf.distribution.HGFDistribution.html
+++ b/generated/pyhgf.distribution/pyhgf.distribution.HGFDistribution.html
@@ -455,11 +455,11 @@
 
  • pyhgf.response.binary_softmax_inverse_temperature
    • 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.distribution/pyhgf.distribution.HGFLogpGradOp.html b/generated/pyhgf.distribution/pyhgf.distribution.HGFLogpGradOp.html
index 8aa664cd6..a6cf06f63 100644
--- a/generated/pyhgf.distribution/pyhgf.distribution.HGFLogpGradOp.html
+++ b/generated/pyhgf.distribution/pyhgf.distribution.HGFLogpGradOp.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.distribution/pyhgf.distribution.hgf_logp.html b/generated/pyhgf.distribution/pyhgf.distribution.hgf_logp.html
index 3d9a354a6..7200b46ad 100644
--- a/generated/pyhgf.distribution/pyhgf.distribution.hgf_logp.html
+++ b/generated/pyhgf.distribution/pyhgf.distribution.hgf_logp.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.math/pyhgf.math.MultivariateNormal.html b/generated/pyhgf.math/pyhgf.math.MultivariateNormal.html
index c38225379..f7ed98092 100644
--- a/generated/pyhgf.math/pyhgf.math.MultivariateNormal.html
+++ b/generated/pyhgf.math/pyhgf.math.MultivariateNormal.html
@@ -54,7 +54,7 @@
     
     
     
-    
+    
   
   
   
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.math/pyhgf.math.binary_surprise_finite_precision.html b/generated/pyhgf.math/pyhgf.math.binary_surprise_finite_precision.html
index ad12da142..0d9cd037f 100644
--- a/generated/pyhgf.math/pyhgf.math.binary_surprise_finite_precision.html
+++ b/generated/pyhgf.math/pyhgf.math.binary_surprise_finite_precision.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.math/pyhgf.math.dirichlet_kullback_leibler.html b/generated/pyhgf.math/pyhgf.math.dirichlet_kullback_leibler.html
index 935278974..3f82ca570 100644
--- a/generated/pyhgf.math/pyhgf.math.dirichlet_kullback_leibler.html
+++ b/generated/pyhgf.math/pyhgf.math.dirichlet_kullback_leibler.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.math/pyhgf.math.gaussian_predictive_distribution.html b/generated/pyhgf.math/pyhgf.math.gaussian_predictive_distribution.html
index 400e09703..59919d6b3 100644
--- a/generated/pyhgf.math/pyhgf.math.gaussian_predictive_distribution.html
+++ b/generated/pyhgf.math/pyhgf.math.gaussian_predictive_distribution.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.plots/pyhgf.plots.plot_correlations.html b/generated/pyhgf.plots/pyhgf.plots.plot_correlations.html
index f08d042ad..c65cfe738 100644
--- a/generated/pyhgf.plots/pyhgf.plots.plot_correlations.html
+++ b/generated/pyhgf.plots/pyhgf.plots.plot_correlations.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.plots/pyhgf.plots.plot_trajectories.html b/generated/pyhgf.plots/pyhgf.plots.plot_trajectories.html
index 14452929d..e03383a82 100644
--- a/generated/pyhgf.plots/pyhgf.plots.plot_trajectories.html
+++ b/generated/pyhgf.plots/pyhgf.plots.plot_trajectories.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.response/pyhgf.response.binary_softmax.html b/generated/pyhgf.response/pyhgf.response.binary_softmax.html
index 5008eea6a..1fe0736a9 100644
--- a/generated/pyhgf.response/pyhgf.response.binary_softmax.html
+++ b/generated/pyhgf.response/pyhgf.response.binary_softmax.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.response/pyhgf.response.binary_softmax_inverse_temperature.html b/generated/pyhgf.response/pyhgf.response.binary_softmax_inverse_temperature.html
index 5aa475cec..c6b987b5b 100644
--- a/generated/pyhgf.response/pyhgf.response.binary_softmax_inverse_temperature.html
+++ b/generated/pyhgf.response/pyhgf.response.binary_softmax_inverse_temperature.html
@@ -55,7 +55,7 @@
     
     
     
-    
+    
     
   
   
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.response/pyhgf.response.first_level_gaussian_surprise.html b/generated/pyhgf.response/pyhgf.response.first_level_gaussian_surprise.html
index f252975e9..fdc22547b 100644
--- a/generated/pyhgf.response/pyhgf.response.first_level_gaussian_surprise.html
+++ b/generated/pyhgf.response/pyhgf.response.first_level_gaussian_surprise.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.response/pyhgf.response.total_gaussian_surprise.html b/generated/pyhgf.response/pyhgf.response.total_gaussian_surprise.html
index 7a4497625..1db3f1d4d 100644
--- a/generated/pyhgf.response/pyhgf.response.total_gaussian_surprise.html
+++ b/generated/pyhgf.response/pyhgf.response.total_gaussian_surprise.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_finite.html b/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_finite.html
index c9d8073f1..b59e50330 100644
--- a/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_finite.html
+++ b/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_finite.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_infinite.html b/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_infinite.html
index 1f15b98ad..105de8b73 100644
--- a/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_infinite.html
+++ b/generated/pyhgf.updates.posterior.binary/pyhgf.updates.posterior.binary.binary_node_update_infinite.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.categorical/pyhgf.updates.posterior.categorical.categorical_input_update.html b/generated/pyhgf.updates.posterior.categorical/pyhgf.updates.posterior.categorical.categorical_input_update.html
index 2bbca66c2..4d5f064e6 100644
--- a/generated/pyhgf.updates.posterior.categorical/pyhgf.updates.posterior.categorical.categorical_input_update.html
+++ b/generated/pyhgf.updates.posterior.categorical/pyhgf.updates.posterior.categorical.categorical_input_update.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update.html b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update.html
index 6d981dd72..925a7a94a 100644
--- a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update.html
+++ b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update_ehgf.html b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update_ehgf.html
index 44774f8e1..4f399ce81 100644
--- a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update_ehgf.html
+++ b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.continuous_node_update_ehgf.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_mean_continuous_node.html b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_mean_continuous_node.html
index 6d7de8a10..715394976 100644
--- a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_mean_continuous_node.html
+++ b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_mean_continuous_node.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_precision_continuous_node.html b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_precision_continuous_node.html
index efc1e2dee..ad38ba82f 100644
--- a/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_precision_continuous_node.html
+++ b/generated/pyhgf.updates.posterior.continuous/pyhgf.updates.posterior.continuous.posterior_update_precision_continuous_node.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction.binary/pyhgf.updates.prediction.binary.binary_state_node_prediction.html b/generated/pyhgf.updates.prediction.binary/pyhgf.updates.prediction.binary.binary_state_node_prediction.html
index c85c8a589..23ca086b6 100644
--- a/generated/pyhgf.updates.prediction.binary/pyhgf.updates.prediction.binary.binary_state_node_prediction.html
+++ b/generated/pyhgf.updates.prediction.binary/pyhgf.updates.prediction.binary.binary_state_node_prediction.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.continuous_node_prediction.html b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.continuous_node_prediction.html
index e8159329d..a362760f2 100644
--- a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.continuous_node_prediction.html
+++ b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.continuous_node_prediction.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_mean.html b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_mean.html
index ad401fed5..6462eab90 100644
--- a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_mean.html
+++ b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_mean.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_precision.html b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_precision.html
index 48c7f1ecd..33e119ab5 100644
--- a/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_precision.html
+++ b/generated/pyhgf.updates.prediction.continuous/pyhgf.updates.prediction.continuous.predict_precision.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_finite_precision.html b/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_finite_precision.html
index 1a8cebe59..df86dfca5 100644
--- a/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_finite_precision.html
+++ b/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_finite_precision.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_infinite_precision.html b/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_infinite_precision.html
index 4f9fe8a1f..588e89bd7 100644
--- a/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_infinite_precision.html
+++ b/generated/pyhgf.updates.prediction_error.inputs.binary/pyhgf.updates.prediction_error.inputs.binary.binary_input_prediction_error_infinite_precision.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_prediction_error.html b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_prediction_error.html
index 1fb014100..2d0bc0434 100644
--- a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_prediction_error.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_value_prediction_error.html b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_value_prediction_error.html
index 9bb70d573..7c010f00c 100644
--- a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_value_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_value_prediction_error.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_volatility_prediction_error.html b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_volatility_prediction_error.html
index 31c9534ab..73f3d2ac4 100644
--- a/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_volatility_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.inputs.continuous/pyhgf.updates.prediction_error.inputs.continuous.continuous_input_volatility_prediction_error.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.nodes.binary/pyhgf.updates.prediction_error.nodes.binary.binary_state_node_prediction_error.html b/generated/pyhgf.updates.prediction_error.nodes.binary/pyhgf.updates.prediction_error.nodes.binary.binary_state_node_prediction_error.html
index 703bd0529..ace6d4abf 100644
--- a/generated/pyhgf.updates.prediction_error.nodes.binary/pyhgf.updates.prediction_error.nodes.binary.binary_state_node_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.nodes.binary/pyhgf.updates.prediction_error.nodes.binary.binary_state_node_prediction_error.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_prediction_error.html b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_prediction_error.html
index 9e029a037..08dc21d7f 100644
--- a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_prediction_error.html
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_value_prediction_error.html b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_value_prediction_error.html
index 3d9460bd1..c5fd1a7d4 100644
--- a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_value_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_value_prediction_error.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_volatility_prediction_error.html b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_volatility_prediction_error.html
index 06b4a1763..8a4c6dd6b 100644
--- a/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_volatility_prediction_error.html
+++ b/generated/pyhgf.updates.prediction_error.nodes.continuous/pyhgf.updates.prediction_error.nodes.continuous.continuous_node_volatility_prediction_error.html
@@ -457,11 +457,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
      
 
    • pyhgf.math.MultivariateNormal
      • 
diff --git a/generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.html b/generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.html
similarity index 85%
rename from generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.html
rename to generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.html
index fbb73dde8..5276a722a 100644
--- a/generated/pyhgf.networks/pyhgf.networks.beliefs_propagation.html
+++ b/generated/pyhgf.utils/pyhgf.utils.beliefs_propagation.html
@@ -8,7 +8,7 @@
     
     
 
-    pyhgf.networks.beliefs_propagation — pyhgf 0.0.18 documentation
+    pyhgf.utils.beliefs_propagation — pyhgf 0.0.18 documentation
   
   
   
@@ -49,11 +49,11 @@
     
     
     
-    
+    
     
     
     
-    
+    
     
   
   
@@ -455,11 +455,11 @@
 
    • pyhgf.response.binary_softmax_inverse_temperature
      • 
 
    
 
 
 
 
@@ -528,11 +528,11 @@
 
                 
    
                   
-  
    
-
    pyhgf.networks.beliefs_propagation#
    
+  
    
+
    pyhgf.utils.beliefs_propagation#
    
 
    
-
    
-pyhgf.networks.beliefs_propagation(attributes: Dict[int, Dict], input_data: Array | ndarray | bool_ | number | bool | int | float | complex, update_sequence: Tuple[Tuple[int, Callable], ...], structure: Tuple[Inputs, Tuple[AdjacencyLists, ...]]) → Tuple[Dict, Dict][source]#
    
+
    
+pyhgf.utils.beliefs_propagation(attributes: Dict[int, Dict], input_data: Array | ndarray | bool_ | number | bool | int | float | complex, update_sequence: Tuple[Tuple[int, Callable], ...], structure: Tuple[Inputs, Tuple[AdjacencyLists, ...]]) → Tuple[Dict, Dict][source]#
    
 
    Update the network’s parameters after observing new data point(s).
    
 
    This function performs the beliefs propagation step at a time t triggered by the
 observation of a new batch of value(s). The way beliefs propagate is defined by the
@@ -589,11 +589,11 @@ 
    pyhgf.networks.beliefs_propagation
       
    
         
    next
    
-        
    pyhgf.networks.trim_sequence
    
+        
    pyhgf.utils.trim_sequence
    
       
    
       
         
@@ -615,14 +615,14 @@ 
    pyhgf.networks.beliefs_propagation
     
   
 
   
    
 
   
    
-    
+    
        Show Source
     
   
    
diff --git a/generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.html b/generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.html
similarity index 89%
rename from generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.html
rename to generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.html
index 41b919b0e..655a6de01 100644
--- a/generated/pyhgf.networks/pyhgf.networks.fill_categorical_state_node.html
+++ b/generated/pyhgf.utils/pyhgf.utils.fill_categorical_state_node.html
@@ -8,7 +8,7 @@
     
     
 
-    pyhgf.networks.fill_categorical_state_node — pyhgf 0.0.18 documentation
+    pyhgf.utils.fill_categorical_state_node — pyhgf 0.0.18 documentation
   
   
   
@@ -49,12 +49,12 @@
     
     
     
-    
+    
     
     
     
-    
-    
+    
+    
   
   
   
@@ -455,11 +455,11 @@
 
  • pyhgf.response.binary_softmax_inverse_temperature
    • 
 
 
 
 
 
    
@@ -528,11 +528,11 @@
 
                 
    
                   
-  
    
-
    pyhgf.networks.fill_categorical_state_node#
    
+  
    
+
    pyhgf.utils.fill_categorical_state_node#
    
 
    
-
    
-pyhgf.networks.fill_categorical_state_node(network: Network, node_idx: int, binary_input_idxs: List[int], binary_parameters: Dict) → Network[source]#
    
+
    
+pyhgf.utils.fill_categorical_state_node(network: Network, node_idx: int, binary_input_idxs: List[int], binary_parameters: Dict) → Network[source]#
    
 
    Generate a binary network implied by categorical state(-transition) nodes.
    
 
    
 
    Parameters:
    
@@ -569,20 +569,20 @@ 
    pyhgf.networks.fill_categorical_state_node
     
       
       
    
         
    previous
    
-        
    pyhgf.networks.list_branches
    
+        
    pyhgf.utils.list_branches
    
       
    
         
     
       
    
         
    next
    
-        
    pyhgf.networks.get_update_sequence
    
+        
    pyhgf.utils.get_update_sequence
    
       
    
       
         
@@ -604,14 +604,14 @@ 
    pyhgf.networks.fill_categorical_state_node
     
   
 
   
    
 
   
    
-    
+    
        Show Source
     
   
    
diff --git a/generated/pyhgf.networks/pyhgf.networks.get_update_sequence.html b/generated/pyhgf.utils/pyhgf.utils.get_update_sequence.html
similarity index 92%
rename from generated/pyhgf.networks/pyhgf.networks.get_update_sequence.html
rename to generated/pyhgf.utils/pyhgf.utils.get_update_sequence.html
index 82c5d1ed5..e53077e2b 100644
--- a/generated/pyhgf.networks/pyhgf.networks.get_update_sequence.html
+++ b/generated/pyhgf.utils/pyhgf.utils.get_update_sequence.html
@@ -8,7 +8,7 @@
     
     
 
-    pyhgf.networks.get_update_sequence — pyhgf 0.0.18 documentation
+    pyhgf.utils.get_update_sequence — pyhgf 0.0.18 documentation
   
   
   
@@ -49,12 +49,12 @@
     
     
     
-    
+    
     
     
     
     
-    
+    
   
   
   
@@ -455,11 +455,11 @@
 
  • pyhgf.response.binary_softmax_inverse_temperature
    • 
 
 
 
 
 
    
@@ -528,11 +528,11 @@
 
                 
    
                   
-  
    
-
    pyhgf.networks.get_update_sequence#
    
+  
    
+
    pyhgf.utils.get_update_sequence#
    
 
    
-
    
-pyhgf.networks.get_update_sequence(network: Network, update_type: str) → List[source]#
    
+
    
+pyhgf.utils.get_update_sequence(network: Network, update_type: str) → List[source]#
    
 
    Generate an update sequence from the network’s structure.
    
 
    This function return an optimized update sequence considering the edges of the
 network. The function ensures that the following principles apply:
@@ -577,12 +577,12 @@ 
    pyhgf.networks.get_update_sequence
     
       
       
    
         
    previous
    
-        
    pyhgf.networks.fill_categorical_state_node
    
+        
    pyhgf.utils.fill_categorical_state_node
    
       
    
         
     pyhgf.networks.get_update_sequence
     
   
 
   
    
 
   
    
-    
+    
        Show Source
     
   
    
diff --git a/generated/pyhgf.networks/pyhgf.networks.list_branches.html b/generated/pyhgf.utils/pyhgf.utils.list_branches.html
similarity index 90%
rename from generated/pyhgf.networks/pyhgf.networks.list_branches.html
rename to generated/pyhgf.utils/pyhgf.utils.list_branches.html
index d20764333..4daf728a7 100644
--- a/generated/pyhgf.networks/pyhgf.networks.list_branches.html
+++ b/generated/pyhgf.utils/pyhgf.utils.list_branches.html
@@ -8,7 +8,7 @@
     
     
 
-    pyhgf.networks.list_branches — pyhgf 0.0.18 documentation
+    pyhgf.utils.list_branches — pyhgf 0.0.18 documentation
   
   
   
@@ -49,12 +49,12 @@
     
     
     
-    
+    
     
     
     
-    
-    
+    
+    
   
   
   
@@ -455,11 +455,11 @@
 
  • pyhgf.response.binary_softmax_inverse_temperature
    • 
 
 
 
 
 
    
@@ -528,11 +528,11 @@
 
                 
    
                   
-  
    
-
    pyhgf.networks.list_branches#
    
+  
    
+
    pyhgf.utils.list_branches#
    
 
    
-
    
-pyhgf.networks.list_branches(node_idxs: List, edges: Tuple, branch_list: List = []) → List[source]#
    
+
    
+pyhgf.utils.list_branches(node_idxs: List, edges: Tuple, branch_list: List = []) → List[source]#
    
 
    Return the branch of a network from a given set of root nodes.
    
 
    This function searches recursively and lists the parents above a given node. If all
 the children of a given parent are on the exclusion list, this parent is also
@@ -571,20 +571,20 @@ 
    pyhgf.networks.list_branches
     
       
       
    
         
    previous
    
-        
    pyhgf.networks.trim_sequence
    
+        
    pyhgf.utils.trim_sequence
    
       
    
         
     
       
    
         
    next
    
-        
    pyhgf.networks.fill_categorical_state_node
    
+        
    pyhgf.utils.fill_categorical_state_node
    
       
    
       
         
@@ -606,14 +606,14 @@ 
    pyhgf.networks.list_branches
     
   
 
   
    
 
   
    
-    
+    
        Show Source
     
   
    
diff --git a/generated/pyhgf.networks/pyhgf.networks.trim_sequence.html b/generated/pyhgf.utils/pyhgf.utils.trim_sequence.html
similarity index 88%
rename from generated/pyhgf.networks/pyhgf.networks.trim_sequence.html
rename to generated/pyhgf.utils/pyhgf.utils.trim_sequence.html
index 62fa54e41..297637482 100644
--- a/generated/pyhgf.networks/pyhgf.networks.trim_sequence.html
+++ b/generated/pyhgf.utils/pyhgf.utils.trim_sequence.html
@@ -8,7 +8,7 @@
     
     
 
-    pyhgf.networks.trim_sequence — pyhgf 0.0.18 documentation
+    pyhgf.utils.trim_sequence — pyhgf 0.0.18 documentation
   
   
   
@@ -49,12 +49,12 @@
     
     
     
-    
+    
     
     
     
-    
-    
+    
+    
   
   
   
@@ -455,11 +455,11 @@
 
  • pyhgf.response.binary_softmax_inverse_temperature
    • 
 
 
 
 
 
    
@@ -528,11 +528,11 @@
 
                 
    
                   
-  
    
-
    pyhgf.networks.trim_sequence#
    
+  
    
+
    pyhgf.utils.trim_sequence#
    
 
    
-
    
-pyhgf.networks.trim_sequence(exclude_node_idxs: List, update_sequence: Tuple[Tuple[int, Callable], ...], edges: Tuple) → Tuple[Tuple[int, Callable], ...][source]#
    
+
    
+pyhgf.utils.trim_sequence(exclude_node_idxs: List, update_sequence: Tuple[Tuple[int, Callable], ...], edges: Tuple) → Tuple[Tuple[int, Callable], ...][source]#
    
 
    Remove steps from an update sequence that depends on a set of nodes.
    
 
    
 
    Parameters:
    
@@ -569,20 +569,20 @@ 
    pyhgf.networks.trim_sequence
     
       
       
    
         
    previous
    
-        
    pyhgf.networks.beliefs_propagation
    
+        
    pyhgf.utils.beliefs_propagation
    
       
    
         
     
       
    
         
    next
    
-        
    pyhgf.networks.list_branches
    
+        
    pyhgf.utils.list_branches
    
       
    
       
         
@@ -604,14 +604,14 @@ 
    pyhgf.networks.trim_sequence
     
   
 
   
    
 
   
    
-    
+    
        Show Source
     
   
    
diff --git a/genindex.html b/genindex.html
index 524dd452e..9cb605adc 100644
--- a/genindex.html
+++ b/genindex.html
@@ -451,7 +451,7 @@ 
    _
    
 
    B
    
 
    
 
    beliefs_propagation(attributes, input_data, ...)
    beliefs_propagation(attributes, input_data, ...)
    		
 
    Update the network's parameters after observing new data point(s).
    		
 
    trim_sequence(exclude_node_idxs, ...)
    trim_sequence(exclude_node_idxs, ...)
    		
 
    Remove steps from an update sequence that depends on a set of nodes.
    		
 
    list_branches(node_idxs, edges[, branch_list])
    list_branches(node_idxs, edges[, branch_list])
    		
 
    Return the branch of a network from a given set of root nodes.
    		
 
    fill_categorical_state_node(network, ...)
    fill_categorical_state_node(network, ...)
    		
 
    Generate a binary network implied by categorical state(-transition) nodes.
    		
 
    get_update_sequence(network, update_type)
    get_update_sequence(network, update_type)
    		
 
    Generate an update sequence from the network's structure.
    		
 
    
 
    
   
   
 
    
diff --git a/notebooks/0.1-Theory.html b/notebooks/0.1-Theory.html
index 50c60ec75..0248a4153 100644
--- a/notebooks/0.1-Theory.html
+++ b/notebooks/0.1-Theory.html
@@ -903,7 +903,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -913,10 +913,10 @@ 
    System configuration
    
diff --git a/notebooks/0.2-Creating_networks.html b/notebooks/0.2-Creating_networks.html
index cb7a346e9..16e98ec25 100644
--- a/notebooks/0.2-Creating_networks.html
+++ b/notebooks/0.2-Creating_networks.html
@@ -736,7 +736,7 @@ 
    Continuous value coupling
-../_images/690788e65a28bf4a04fd2ef6be113e78e08c0db2354106f5136f12e9db40561f.png
+../_images/de2a3753c892d57c1524c4594968017abcb7099490429b8d6dc99c85016b55b0.png
 
    
 
    
 
    
@@ -1066,7 +1066,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -1077,9 +1077,9 @@ 
    System configuration
    
diff --git a/notebooks/0.3-Generalised_filtering.html b/notebooks/0.3-Generalised_filtering.html
index 27f96ef20..5ae030eb9 100644
--- a/notebooks/0.3-Generalised_filtering.html
+++ b/notebooks/0.3-Generalised_filtering.html
@@ -503,7 +503,7 @@
 from matplotlib.ticker import MultipleLocator
 from pyhgf.math import MultivariateNormal, Normal, gaussian_predictive_distribution
 from pyhgf.model import HGF
-from pyhgf.networks import beliefs_propagation
+from pyhgf.utils import beliefs_propagation
 from scipy.special import gammaln
 from scipy.stats import norm, t
 
@@ -935,7 +935,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
diff --git a/notebooks/1.1-Binary_HGF.html b/notebooks/1.1-Binary_HGF.html
index 4b0be9102..669b3d4b4 100644
--- a/notebooks/1.1-Binary_HGF.html
+++ b/notebooks/1.1-Binary_HGF.html
@@ -51,7 +51,7 @@
     
     
     
-    
+    
     
     
     
@@ -792,19 +792,22 @@ 
    Sampling
   self.pid = os.fork()
 
    
 
    
-
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
   self.pid = os.fork()
 
    
 
    
 
    
 
     
    
-
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 16 seconds.
+
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 17 seconds.
 
    
 
    
 
    We recommend running at least 4 chains for robust computation of convergence diagnostics
 
    
 
    
+
    The rhat statistic is larger than 1.01 for some parameters. This indicates problems during sampling. See https://arxiv.org/abs/1903.08008 for details
+
    
+
    
 
    
 
    
 
    
@@ -815,7 +818,7 @@ 
    Sampling
 
    
 
    
 
    
-../_images/f2a4964ebba623b68f69bf0648e47b01f16cf56116c8edc7a12fe1b6b40aded9.png
+../_images/1dc70311198250c983a638d2c1d50fb69da11820aa3a529a49793e9245e81330.png
 
    
 
    
 
@@ -853,7 +856,7 @@ 
    Using the learned parameters
-../_images/0338347516b69db9fbb7fd68de9936ee04c135283f4891a80839db1f98bafe19.png
+../_images/a8da50c1a0b0b4b2f24551820095b2bd32e47462dc0951880adae3b8d4e192e7.png
 
    
 
    
 
    
@@ -863,7 +866,7 @@ 
    Using the learned parameters
-
    Array(202.5304, dtype=float32)
+
    Array(202.53049, dtype=float32)
 
    
 
    
 
    
@@ -915,7 +918,7 @@ 
    Visualizing the model
-../_images/69539e2739458d7218e514133841304a4e4b0eb711fc8054497123f2e226d095.svg
    
+../_images/906f003ac3c62510821da40b51513f921c716a616f423184ce543353e719929c.svg
    
 
    
 
 
    
@@ -944,7 +947,11 @@ 
    Sampling#
   self.pid = os.fork()
 
    
 
    
-
    
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+  self.pid = os.fork()
+
    
+
    
+
    
 
     
    
 
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 21 seconds.
@@ -963,7 +970,7 @@ 
    Sampling#
 
    
 
    
 
    
-../_images/1bb83169c1da5f7e45ce881565950dbcda92412214e876ba70af0fbcafd9207b.png
+../_images/064a095c93a11062f592f9a9f2d97c3364784ad20d529e434bf01ae4e005c10e.png
 
    
 
    
 
@@ -1002,7 +1009,7 @@ 
    Using the learned parameters
-../_images/e8d64ae897cd750329a324b1cf1290d9cb37c7c1532b70e75f19c22fd6d6e8d6.png
+../_images/248b4b53ded9a8deaead9f14a8c327dca3af86e7a2b8ce7a5823d86c4ca608d7.png
 
    
 
    
 
    
@@ -1012,7 +1019,7 @@ 
    Using the learned parameters
-
    Array(203.01108, dtype=float32)
+
    Array(203.01868, dtype=float32)
 
    
 
    
 
    
@@ -1030,7 +1037,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -1040,11 +1047,11 @@ 
    System configurationSimulating a dataset
 
    
 
    
-../_images/32259d128425fa615aea6e9a2c92a8714cd998e7593afba19c3fb234a4d86cd8.png
+../_images/036707b8ed10e44f3def5a2175695c05d0cc1a35ace9544ae661b4a283c9beca.png
 
    
 
    
 
    
@@ -689,7 +689,7 @@ 
    Fitting the model forwards
-../_images/c325e818c58e0d5d0b3bc3d44c5023c9cfcd5870e0f7de2d258095eb97ae384e.png
+../_images/c9fd2b0dc5a0be69606e1b730cf0655ca964fc5dc28bc3b5da08bbf205837d6d.png
 
    
 
    
 
@@ -837,7 +837,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -847,14 +847,14 @@ 
    System configuration
    
diff --git a/notebooks/1.3-Continuous_HGF.html b/notebooks/1.3-Continuous_HGF.html
index 2fbb590b4..35fc29fac 100644
--- a/notebooks/1.3-Continuous_HGF.html
+++ b/notebooks/1.3-Continuous_HGF.html
@@ -51,7 +51,7 @@
     
     
     
-    
+    
     
     
     
@@ -846,7 +846,7 @@ 
    Sampling
   self.pid = os.fork()
 
    
 
    
-
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
   self.pid = os.fork()
 
    
 
    
@@ -869,7 +869,7 @@ 
    Sampling
 
    
 
    
 
    
-../_images/6870c878dfa8be2a489ffd7c0a9945c167260725be27e94b8c323d315acd9f16.png
+../_images/fc9c9d0ad7db3f8618a8fab2954880ab258dbe4672cdeda6d28e830f0e0fb36a.png
 
    
 
    
 
@@ -904,7 +904,7 @@ 
    Using the learned parameters
-../_images/99baaf96994441c801b09e398badaa2fec3fa62b5da6d4541c28b2374857cc78.png
+../_images/912fffdcd2054c64eed5d2aa8bf4727c5e1de8d1da7009137538546b84545cba.png
 
    
 
    
 
    
@@ -914,7 +914,7 @@ 
    Using the learned parameters
-
    Array(-1106.1003, dtype=float32)
+
    Array(-1106.1105, dtype=float32)
 
    
 
    
 
    
@@ -993,7 +993,11 @@ 
    Sampling#
   self.pid = os.fork()
 
    
 
    
-
    
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+  self.pid = os.fork()
+
    
+
    
+
    
 
     
    
 
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 22 seconds.
@@ -1012,7 +1016,7 @@ 
    Sampling#
 
    
 
    
 
    
-../_images/859bec03d8983e9c387967887e1c84c70dcc3933aa89f33eaea6178dc57da837.png
+../_images/bcd503c8f4461dd08d4b1cd18167f2d2c9e512d2ff24463158c6fc8f90b98fa3.png
 
    
 
    
 
@@ -1046,7 +1050,7 @@ 
    Using the learned parameters
-../_images/ec45c913dddfe05083a32f5a73116e68992ff0978b7f3ba77f4ba143eea09cc0.png
+../_images/16b6d00f943b9b8f127662c2a34f0a6eb4a54ae97fd7dfe4473a11ab262bc786.png
 
    
 
    
 
    
@@ -1056,7 +1060,7 @@ 
    Using the learned parameters
-
    Array(-1118.0167, dtype=float32)
+
    Array(-1118.0038, dtype=float32)
 
    
 
    
 
    
@@ -1074,7 +1078,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -1084,9 +1088,9 @@ 
    System configurationvar togglebuttonSelector = '.toggle, .admonition.dropdown';
     
     
-    
+    
     
     
     
@@ -888,13 +888,13 @@ 
    Recovering HGF parameters from the observed behaviors
    NUTS: [tonic_volatility_2]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    
+
    
 
    
 
    
 
    
@@ -937,19 +937,19 @@ 
    Recovering HGF parameters from the observed behaviors
     
       tonic_volatility_2
-      -3.948
-      0.507
-      -4.858
-      -2.938
+      -3.957
+      0.491
+      -4.837
+      -2.974
       0.012
       0.009
-      1757.0
-      2514.0
+      1597.0
+      2576.0
       1.0
     
   
 
-
    ../_images/2c05c24fd9a88f8b89577d0ca0dcd551e04308054d1b82ff87bc5e37b12d75bb.png
+
    ../_images/0539b59bce54e24aa674cfd43a8494bed83174f6ce6c90341820bfbf525e1f23.png
 
    
 
    
 
    The results above indicate that given the responses provided by the participant, the most likely values for the parameter \(\omega_2\) are between -4.9 and -3.1, with a mean at -3.9 (you can find slightly different values if you sample different actions from the decisions function). We can consider this as an excellent estimate given the sparsity of the data, and the complexity of the model.
    
@@ -977,7 +977,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -987,12 +987,12 @@ 
    System configuration
    
diff --git a/notebooks/3-Multilevel_HGF.html b/notebooks/3-Multilevel_HGF.html
index 79f31f78e..88108fd81 100644
--- a/notebooks/3-Multilevel_HGF.html
+++ b/notebooks/3-Multilevel_HGF.html
@@ -51,7 +51,7 @@
     
     
     
-    
+    
     
     
     
@@ -707,7 +707,7 @@ 
    Plot the computational graph
-../_images/696a07dc07aeeb78568195b4cd27da10c346b2f3696efa9446d59734f805f924.svg
    
+../_images/0b97b076146b6fa4943dcd3dec35240d123dfd9ae79c99489d37f4c1181370f8.svg
    
 
    
 
 
    
@@ -732,10 +732,10 @@ 
    Sampling
 
    NUTS: [mu_volatility, sigma_volatility, volatility, mu_temperature, sigma_temperature, inverse_temperature]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
 
 
    
@@ -748,7 +748,7 @@ 
    Visualization of the posterior distributions
-../_images/9dd169223f849709d0e96f9e2b359b7e54bb489c486433223b1de934ec60675d.png
+../_images/d2c8100ed99add21a983cd1ff589d723b8f399879fe56560c344134d58ba7733.png
 
 
 
    The reference values on both posterior distributions indicate the mean of the distribution used for simulation.
    
@@ -764,7 +764,7 @@ 
    System configuration
 
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -774,10 +774,10 @@ 
    System configurationvar togglebuttonSelector = '.toggle, .admonition.dropdown';
     
     
-    
+    
     
     
     
@@ -664,10 +664,10 @@ 
    Inference from the simulated behaviours
    NUTS: [censored_volatility, inverse_temperature]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
    
 
    
 
    
@@ -723,7 +723,7 @@ 
    Visualizing parameters recovery
-../_images/8e13d3fa71ea9b734811483035e21406ecf61b532e57f8699aebe920d35e0fb9.png
+../_images/e8375c0bab4b282f149e887dfc886c14e315fc329203e713d139911df5fa8147.png
 
 
 
    
@@ -738,7 +738,7 @@ 
    System configuration
 
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -748,13 +748,13 @@ 
    System configuration
    
diff --git a/notebooks/Example_1_Heart_rate_variability.html b/notebooks/Example_1_Heart_rate_variability.html
index 1064b2bbc..c4f2b00a5 100644
--- a/notebooks/Example_1_Heart_rate_variability.html
+++ b/notebooks/Example_1_Heart_rate_variability.html
@@ -49,7 +49,7 @@
     
     
     
-    
+    
     
     
     
@@ -555,16 +555,16 @@ 
    Loading and preprocessing physiological recording
    Downloading ECG channel:   0%|          | 0/2 [00:00<?, ?it/s]
 
    
 
    
-
    Downloading ECG channel:  50%|█████     | 1/2 [00:00<00:00,  1.45it/s]
+
    Downloading ECG channel:  50%|█████     | 1/2 [00:00<00:00,  1.72it/s]
 
    
 
    
-
    Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  1.45it/s]
+
    Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  1.72it/s]
 
    
 
    
-
    Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.60it/s]
+
    Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.78it/s]
 
    
 
    
-
    Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.57it/s]
+
    Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.77it/s]
 
    
 
    
 
    
@@ -638,7 +638,7 @@ 
    Model#<
 
    
 
    
 
    
-../_images/8fc9c210ab62f5dd9a3be3ce533d3c8c7ee05351b66a0f94da4f8a26be10ae39.svg
    
+../_images/8f02834ccc45a1fbb4bd4aabfac2d75a89a86b3ef90438ded772ac7bf43de688.svg
    
 
    
 
    
 
    
@@ -664,7 +664,7 @@ 
    Model#<
   self.pid = os.fork()
 
    
 
    
-
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
   self.pid = os.fork()
 
    
 
    
@@ -687,7 +687,7 @@ 
    Model#<
 
    
 
    
 
    
-../_images/d612078ec9c0e0c6a3eedf48161006c61eca0e356ff0b881f6efc2e834dfa9e3.png
+../_images/8493898cebfecbc8f291a4b7247f316d2edd76667ee28805648395d96146231f.png
 
    
 
    
 
    
@@ -719,7 +719,7 @@ 
    Model#<
 
    
 
    
 
    
-../_images/bf3cf6b3bd9ee098f466293af2af94a39e55178a860be856e5be6e7aee72346e.png
+../_images/7dfea04c749d084b7f2f78506c67509c43f70475026a98ef0a7073888e3358f2.png
 
    
 
    
 
@@ -734,7 +734,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -744,12 +744,12 @@ 
    System configuration
    
diff --git a/notebooks/Example_2_Input_node_volatility_coupling.html b/notebooks/Example_2_Input_node_volatility_coupling.html
index fff0d4550..9429da274 100644
--- a/notebooks/Example_2_Input_node_volatility_coupling.html
+++ b/notebooks/Example_2_Input_node_volatility_coupling.html
@@ -681,7 +681,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -692,11 +692,11 @@ 
    System configuration
    
diff --git a/notebooks/Example_3_Multi_armed_bandit.html b/notebooks/Example_3_Multi_armed_bandit.html
index e6aa3d1cd..3da28bb5e 100644
--- a/notebooks/Example_3_Multi_armed_bandit.html
+++ b/notebooks/Example_3_Multi_armed_bandit.html
@@ -51,7 +51,7 @@
     
     
     
-    
+    
     
     
     
@@ -821,10 +821,10 @@ 
    Parameter recovery
 
    Real-time decision and belief updating#
    
-
    We can implement this process using the pyhgf.networks.beliefs_propagation() function. In other models, this step is called sequentially in a jax.lax.scan() loop, but we can also use it for a single-step update.
    
+
    We can implement this process using the pyhgf.networks.beliefs_propagation() function. In other models, this step is called sequentially in a jax.lax.scan() loop, but we can also use it for a single-step update.
    
 
    
 
    
-
    from pyhgf.networks import beliefs_propagation
+
    from pyhgf.utils import beliefs_propagation
 
    
 
    
 
    
@@ -1081,16 +1081,16 @@ 
    Bayesian inference
    NUTS: [omega]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 25 seconds.
+
    Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 26 seconds.
 
    
 
    
-
    There were 2 divergences after tuning. Increase `target_accept` or reparameterize.
+
    There were 5 divergences after tuning. Increase `target_accept` or reparameterize.
 
    
 
    
 
    We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -1108,7 +1108,7 @@ 
    Bayesian inference
-../_images/20c0c4ac2ca3286c3e51662e43b2df59e5bbd6af5d76ae09b0edfdbae567107a.png
+../_images/e0689a235c8e19c70d4f74aad005de618670a2fab15020894bb6a96a16ed5343.png
 
    
 
    
 
@@ -1123,7 +1123,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -1133,14 +1133,14 @@ 
    System configuration
    
diff --git a/notebooks/Exercise_1_Using_the_HGF.html b/notebooks/Exercise_1_Using_the_HGF.html
index 4d3cb7189..0ffa953ab 100644
--- a/notebooks/Exercise_1_Using_the_HGF.html
+++ b/notebooks/Exercise_1_Using_the_HGF.html
@@ -51,7 +51,7 @@
     
     
     
-    
+    
     
     
     
@@ -758,7 +758,7 @@ 
    Parameters optimization
    
 
    
-
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
   self.pid = os.fork()
 
    
 
    
@@ -771,7 +771,7 @@ 
    Parameters optimization
 
    
 
    
-../_images/83e00be6711243ffbc817579224b2318723478e85e9666ffbc281549d319d0e1.png
+../_images/aef0c14fc621cd8eaaf348a5bbc80ddb0caa64ab4f3c814a8b36807cb91222e0.png
 
    
 
    
 
    
@@ -813,15 +813,15 @@ 
    Parameters optimization
     
       tonic_volatility_1
-      -5.988
-      0.919
-      -7.608
-      -4.236
-      0.027
-      0.019
-      1255.0
-      1111.0
-      1.0
+      -5.943
+      0.946
+      -7.714
+      -4.169
+      0.03
+      0.022
+      1079.0
+      718.0
+      1.01
     
   
 
@@ -1160,19 +1160,11 @@ 
    Biased random{"version_major": 2, "version_minor": 0, "model_id": "6b990c3878b142398abc7fde6e6859b8"}
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
   self.pid = os.fork()
 
    
 
    
-
    
-
    -
    
-
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 35 seconds.
-
    
 
    
-
    -
    
-
    
 
    
 
    
 
    
@@ -1181,7 +1173,7 @@ 
    Biased random
-../_images/ae7fc8bf131ed37e77411966d824d325a0233077c9bdc8813587730d0ad207a8.png
+../_images/961af07fc8eca6d3dc1184d57c097db7ad086431fc2972c9a6c3aa606e2fcc19.png
 
    
 
    
 
    Assess model fitting, here using leave-one-out cross-validation from the Arviz library.
    
@@ -1196,8 +1188,8 @@ 
    Biased random
    Computed from 4000 posterior samples and 1.0 observations log-likelihood matrix.
 
          Estimate       SE
-elpd_loo  -222.60     0.00
-p_loo        0.83        -
+elpd_loo  -222.44     0.00
+p_loo        0.70        -
 
 There has been a warning during the calculation. Please check the results.
 ------
@@ -1206,8 +1198,8 @@ 
    Biased random{"version_major": 2, "version_minor": 0, "model_id": "f7fc458c340943bbb47a1a4f3f40cd97"}
    
-
    -
    
-
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 102 seconds.
+
    /opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/multiprocessing/popen_fork.py:66: RuntimeWarning: os.fork() was called. os.fork() is incompatible with multithreaded code, and JAX is multithreaded, so this will likely lead to a deadlock.
+  self.pid = os.fork()
 
    
 
    
-
    -
    
-
    
+
    
 
    
 
    
 
    
@@ -1323,7 +1311,7 @@ 
    Rescorla-Wagner
-../_images/11a9faf08d56c7ce82398f74056da811f13f520c27b995ba1c6fb8d141c8f236.png
+../_images/0080536a5a3361977942adea0b4a56460bd70efb2239c452abaa5cd8eb5da53d.png
 
    
 
    
 
    
@@ -1337,8 +1325,8 @@ 
    Rescorla-Wagner
    Computed from 4000 posterior samples and 1.0 observations log-likelihood matrix.
 
          Estimate       SE
-elpd_loo  -103.81     0.00
-p_loo        0.56        -
+elpd_loo  -103.85     0.00
+p_loo        0.61        -
 
 There has been a warning during the calculation. Please check the results.
 ------
@@ -1458,27 +1446,24 @@ 
    Two-level HGF
    NUTS: [tonic_volatility_2]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 35 seconds.
+
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 32 seconds.
 
    
 
    
 
     
    
-
    There were 1 divergences after tuning. Increase `target_accept` or reparameterize.
-
    
-
    
-
    
+
    
 
    
 
    
 
    
@@ -1487,7 +1472,7 @@ 
    Two-level HGF
-../_images/dfaef3e2dfb543fbb107ecafcebfa958877da464c77ba5ea929d4e1906e7fb89.png
+../_images/c28b8afe937738d37929b3a17e73b0fdc31fa1f82bb478fb4487c0d4eb2c9d9b.png
 
    
 
    
 
    
@@ -1501,7 +1486,7 @@ 
    Two-level HGF
    Computed from 4000 posterior samples and 1.0 observations log-likelihood matrix.
 
          Estimate       SE
-elpd_loo  -114.26     0.00
+elpd_loo  -114.27     0.00
 p_loo        0.95        -
 
 There has been a warning during the calculation. Please check the results.
@@ -1581,24 +1566,24 @@ 
    Three-level HGF
    NUTS: [tonic_volatility_2]
 
    
 
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    
+
    
 
     
    
-
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 37 seconds.
+
    Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 38 seconds.
 
    
 
    
 
     
    
-
    There were 15 divergences after tuning. Increase `target_accept` or reparameterize.
+
    There were 7 divergences after tuning. Increase `target_accept` or reparameterize.
 
    
 
    
 
    
@@ -1611,7 +1596,7 @@ 
    Three-level HGF
-../_images/6c3d8c8e6035f505a977f4da93af903ae7337fe350b9582c4841024feb855bbd.png
+../_images/297f3909d308c95fbbbce1266f761eebbda8cbb8657aab611e39a0617b402dda.png
 
    
 
    
 
    
@@ -1625,8 +1610,8 @@ 
    Three-level HGF
    Computed from 4000 posterior samples and 1.0 observations log-likelihood matrix.
 
          Estimate       SE
-elpd_loo  -113.70     0.00
-p_loo        0.76        -
+elpd_loo  -114.14     0.00
+p_loo        1.16        -
 
 There has been a warning during the calculation. Please check the results.
 ------
@@ -1689,8 +1674,8 @@ 
    Three-level HGF
-../_images/70d46d755d70923d1a888ec0116b938eab920d3b8b30a083bfd4a03505b5afa8.png
+../_images/81fdce32cc19746a06503344b5c9b995f6227a1db7c5ebad6faca00c8668def1.png
 
    
 
    
 
@@ -1832,7 +1817,7 @@ 
    System configuration
 
    
 
    
-
    Last updated: Thu May 23 2024
+
    Last updated: Fri May 24 2024
 
 Python implementation: CPython
 Python version       : 3.12.3
@@ -1842,15 +1827,15 @@ 
    System configuration
    
diff --git a/objects.inv b/objects.inv
index bc31aaee4..f88ae5525 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index bca6be893..5a459c7f0 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"A multilevel binary HGF": [[58, "a-multilevel-binary-hgf"]], "API": [[0, "api"]], "Acknowledgments": [[49, "acknowledgments"]], "Add data": [[54, "add-data"], [54, "id4"], [56, "add-data"], [56, "id3"]], "Adding a drift to the random walk": [[51, "adding-a-drift-to-the-random-walk"]], "An introduction to Hierarchical Gaussian Filters through practical exercises": [[63, "an-introduction-to-hierarchical-gaussian-filters-through-practical-exercises"]], "Autoregressive processes": [[51, "autoregressive-processes"]], "Bayesian inference": [[62, "bayesian-inference"]], "Bayesian reinforcement learning: the binary HGF": [[63, "bayesian-reinforcement-learning-the-binary-hgf"]], "Belief updating under uncertainty: the continuous Hierarchical Gaussian Filter": [[63, "belief-updating-under-uncertainty-the-continuous-hierarchical-gaussian-filter"]], "Biased random": [[63, "biased-random"]], "Binary inputs": [[0, "binary-inputs"]], "Binary nodes": [[0, "binary-nodes"], [0, "id1"]], "Binary state nodes": [[0, "binary-state-nodes"]], "Bivariate normal distribution": [[53, "bivariate-normal-distribution"]], "Categorical nodes": [[0, "categorical-nodes"]], "Continuous inputs": [[0, "continuous-inputs"]], "Continuous nodes": [[0, "continuous-nodes"], [0, "id2"]], "Continuous state nodes": [[0, "continuous-state-nodes"]], "Continuous value coupling": [[52, "continuous-value-coupling"]], "Continuous volatility coupling": [[52, "continuous-volatility-coupling"]], "Coupling with binary nodes": [[52, "coupling-with-binary-nodes"]], "Create the model": [[54, "create-the-model"], [54, "id3"], [56, "create-the-model"], [56, "id2"]], "Creating a new response function": [[57, "creating-a-new-response-function"]], "Creating a new response function: the binary surprise": [[57, "creating-a-new-response-function-the-binary-surprise"]], "Creating and manipulating networks of probabilistic nodes": [[52, "creating-and-manipulating-networks-of-probabilistic-nodes"]], "Creating custom update functions": [[52, "creating-custom-update-functions"]], "Creating custom update sequences": [[52, "creating-custom-update-sequences"]], "Creating probabilistic nodes": [[52, "creating-probabilistic-nodes"]], "Creating the decision rule": [[57, "creating-the-decision-rule"]], "Creating the model": [[54, "creating-the-model"], [54, "id7"], [56, "creating-the-model"], [56, "id5"]], "Creating the probabilistic network": [[55, "creating-the-probabilistic-network"]], "Decision rule": [[62, "decision-rule"]], "Distribution": [[0, "distribution"]], "Dynamic assignation of update sequences": [[52, "dynamic-assignation-of-update-sequences"]], "Dynamic beliefs updating": [[51, "dynamic-beliefs-updating"]], "Embeding Hierarchical Gaussian Filters in a multilevel Bayesian model": [[58, "embeding-hierarchical-gaussian-filters-in-a-multilevel-bayesian-model"]], "Example 1: Bayesian filtering of cardiac volatility": [[60, "example-1-bayesian-filtering-of-cardiac-volatility"]], "Example 2: Estimating the mean and precision of an input node": [[61, "example-2-estimating-the-mean-and-precision-of-an-input-node"]], "Example 3: A multi-armed bandit task with independent rewards and punishments": [[62, "example-3-a-multi-armed-bandit-task-with-independent-rewards-and-punishments"]], "Exercise 1": [[63, null]], "Exercise 2": [[63, null]], "Exercise 3": [[63, null]], "Exercises": [[50, "exercises"]], "Exercises 4": [[63, null]], "Exercises 5": [[63, null]], "Filtering the Sufficient Statistics of a Non-Stationary Distribution": [[53, "filtering-the-sufficient-statistics-of-a-non-stationary-distribution"]], "Filtering the Sufficient Statistics of a Stationary Distribution": [[53, "filtering-the-sufficient-statistics-of-a-stationary-distribution"]], "Fitting the binary HGF with fixed parameters": [[54, "fitting-the-binary-hgf-with-fixed-parameters"]], "Fitting the continuous HGF with fixed parameters": [[56, "fitting-the-continuous-hgf-with-fixed-parameters"]], "Fitting the model forwards": [[55, "fitting-the-model-forwards"]], "From Reinforcement Learning to Generalised Bayesian Filtering": [[53, "from-reinforcement-learning-to-generalised-bayesian-filtering"]], "Gaussian Random Walks": [[51, "gaussian-random-walks"]], "Gaussian random walks": [[63, "gaussian-random-walks"]], "Getting started": [[49, "getting-started"]], "Glossary": [[51, "glossary"], [57, "glossary"]], "How does it work?": [[49, "how-does-it-work"]], "How to cite?": [[1, "how-to-cite"]], "Imports": [[54, "imports"]], "Inference from the simulated behaviours": [[59, "inference-from-the-simulated-behaviours"]], "Inference using MCMC sampling": [[55, "inference-using-mcmc-sampling"]], "Inputs": [[0, "inputs"]], "Installation": [[49, "installation"]], "Introduction to the Generalised Hierarchical Gaussian Filter": [[51, "introduction-to-the-generalised-hierarchical-gaussian-filter"]], "Kown mean, unknown precision": 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\ No newline at end of file
+Search.setIndex({"alltitles": {"A multilevel binary HGF": [[58, "a-multilevel-binary-hgf"]], "API": [[0, "api"]], "Acknowledgments": [[49, "acknowledgments"]], "Add data": [[54, "add-data"], [54, "id4"], [56, "add-data"], [56, "id3"]], "Adding a drift to the random walk": [[51, "adding-a-drift-to-the-random-walk"]], "An introduction to Hierarchical Gaussian Filters through practical exercises": [[63, "an-introduction-to-hierarchical-gaussian-filters-through-practical-exercises"]], "Autoregressive processes": [[51, "autoregressive-processes"]], "Bayesian inference": [[62, "bayesian-inference"]], "Bayesian reinforcement learning: the binary HGF": [[63, "bayesian-reinforcement-learning-the-binary-hgf"]], "Belief updating under uncertainty: the continuous Hierarchical Gaussian Filter": [[63, "belief-updating-under-uncertainty-the-continuous-hierarchical-gaussian-filter"]], "Biased random": [[63, "biased-random"]], "Binary inputs": [[0, "binary-inputs"]], "Binary nodes": [[0, "binary-nodes"], [0, "id1"]], "Binary state nodes": [[0, "binary-state-nodes"]], "Bivariate normal distribution": [[53, "bivariate-normal-distribution"]], "Categorical nodes": [[0, "categorical-nodes"]], "Continuous inputs": [[0, "continuous-inputs"]], "Continuous nodes": [[0, "continuous-nodes"], [0, "id2"]], "Continuous state nodes": [[0, "continuous-state-nodes"]], "Continuous value coupling": [[52, "continuous-value-coupling"]], "Continuous volatility coupling": [[52, "continuous-volatility-coupling"]], "Coupling with binary nodes": [[52, "coupling-with-binary-nodes"]], "Create the model": [[54, "create-the-model"], [54, "id3"], [56, "create-the-model"], [56, "id2"]], "Creating a new response function": [[57, "creating-a-new-response-function"]], "Creating a new response function: the binary surprise": [[57, "creating-a-new-response-function-the-binary-surprise"]], "Creating and manipulating networks of probabilistic nodes": [[52, "creating-and-manipulating-networks-of-probabilistic-nodes"]], "Creating custom update functions": [[52, "creating-custom-update-functions"]], "Creating custom update sequences": [[52, "creating-custom-update-sequences"]], "Creating probabilistic nodes": [[52, "creating-probabilistic-nodes"]], "Creating the decision rule": [[57, "creating-the-decision-rule"]], "Creating the model": [[54, "creating-the-model"], [54, "id7"], [56, "creating-the-model"], [56, "id5"]], "Creating the probabilistic network": [[55, "creating-the-probabilistic-network"]], "Decision rule": [[62, "decision-rule"]], "Distribution": [[0, "distribution"]], "Dynamic assignation of update sequences": [[52, "dynamic-assignation-of-update-sequences"]], "Dynamic beliefs updating": [[51, "dynamic-beliefs-updating"]], "Embeding Hierarchical Gaussian Filters in a multilevel Bayesian model": [[58, "embeding-hierarchical-gaussian-filters-in-a-multilevel-bayesian-model"]], "Example 1: Bayesian filtering of cardiac volatility": [[60, "example-1-bayesian-filtering-of-cardiac-volatility"]], "Example 2: Estimating the mean and precision of an input node": [[61, "example-2-estimating-the-mean-and-precision-of-an-input-node"]], "Example 3: A multi-armed bandit task with independent rewards and punishments": [[62, "example-3-a-multi-armed-bandit-task-with-independent-rewards-and-punishments"]], "Exercise 1": [[63, null]], "Exercise 2": [[63, null]], "Exercise 3": [[63, null]], "Exercises": [[50, "exercises"]], "Exercises 4": [[63, null]], "Exercises 5": [[63, null]], "Filtering the Sufficient Statistics of a Non-Stationary Distribution": [[53, "filtering-the-sufficient-statistics-of-a-non-stationary-distribution"]], "Filtering the Sufficient Statistics of a Stationary Distribution": [[53, "filtering-the-sufficient-statistics-of-a-stationary-distribution"]], "Fitting the binary HGF with fixed parameters": [[54, "fitting-the-binary-hgf-with-fixed-parameters"]], "Fitting the continuous HGF with fixed parameters": 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