shorten the intro

_build/html/README.html

@@ -97,9 +97,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="chapters/ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="chapters/hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -108,58 +113,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hmm.html">
+    <a class="reference internal" href="chapters/hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="chapters/hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -190,8 +148,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -222,8 +180,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -249,8 +207,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -301,8 +259,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/_sources/chapters/scratch.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "8effb7c4",
+   "id": "6986d0f3",
    "metadata": {},
    "source": [
     "(ch:intro)=\n",
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "a9311a84",
+   "id": "5d887c30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "41386a79",
+   "id": "57031b40",
    "metadata": {},
    "outputs": [
     {
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "55b29f42",
+   "id": "5e9e11d3",
    "metadata": {},
    "outputs": [
     {
@@ -113,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6c78ea7d",
+   "id": "264fb6e0",
    "metadata": {},
    "source": [
     "## Images\n",

_build/html/_sources/chapters/ssm/deep.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Deep SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/hsmm.ipynb

@@ -1,33 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Hidden Semi-Markov Models\n",
-    "\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/lgssm.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Linear Gaussian SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/nongauss.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#  Non-Gaussian SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/nonlin.ipynb

@@ -1,32 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Non-Linear Gaussian SSMs\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/rnn.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Recurrent Neural Networks\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/_sources/chapters/ssm/ssm_index.md

@@ -1,7 +0,0 @@
-
-
-(ch:ssm)=
-# Introduction 
-
-```{tableofcontents}
-```

_build/html/_sources/chapters/ssm/switching.ipynb

@@ -1,44 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Switching SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Jump Markov Linear Dynamical Systems"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/html/bib.html

@@ -98,9 +98,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="chapters/ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="chapters/hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -109,58 +114,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hmm.html">
+    <a class="reference internal" href="chapters/hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="chapters/hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -191,8 +149,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -223,8 +181,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -250,8 +208,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -302,8 +260,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/adf/adf_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/blank.html

@@ -97,9 +97,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -108,58 +113,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="ssm/hmm.html">
+    <a class="reference internal" href="hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -190,8 +148,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -222,8 +180,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -249,8 +207,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -301,8 +259,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/bnp/bnp_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/changepoint/changepoint_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/control/control_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/ensemble/ensemble_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/extended/extended_filter.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="extended_index.html">
    Extended (linearized) methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/extended/extended_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="current reference internal" href="#">
    Extended (linearized) methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/extended/extended_parallel.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="extended_index.html">
    Extended (linearized) methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/extended/extended_smoother.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="extended_index.html">
    Extended (linearized) methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/gp/gp_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/ssm/hmm.html

@@ -53,8 +53,8 @@ const thebe_selector_output = ".output, .cell_output"
     <script async="async" src="../../_static/sphinx-thebe.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Hidden Semi-Markov Models" href="hsmm.html" />
-    <link rel="prev" title="Introduction" href="ssm_index.html" />
+    <link rel="next" title="HMM filtering (forwards algorithm)" href="hmm_filter.html" />
+    <link rel="prev" title="Inference in discrete SSMs" href="hmm_index.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
     
@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
+  <a class="reference internal" href="hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -115,74 +120,27 @@ const thebe_selector_output = ".output, .cell_output"
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
+    <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
+    <a class="reference internal" href="hmm_smoother.html">
      HMM smoothing (forwards-backwards algorithm)
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
+    <a class="reference internal" href="hmm_viterbi.html">
      Viterbi algorithm
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
+    <a class="reference internal" href="hmm_parallel.html">
      Parallel HMM  smoothing
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
+    <a class="reference internal" href="hmm_sampling.html">
      Forwards-filtering backwards-sampling algorithm
     </a>
    </li>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -417,7 +375,7 @@ const thebe_selector_output = ".output, .cell_output"
         <!-- ipynb file if we had a myst markdown file -->
         
         <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/hmm.ipynb"><button type="button"
+        <a class="dropdown-buttons" href="../../_sources/chapters/hmm/hmm.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
                 data-placement="left">.ipynb</button></a>
         <!-- Download PDF via print -->
@@ -437,7 +395,7 @@ const thebe_selector_output = ".output, .cell_output"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/hmm.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/hmm/hmm.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
         
@@ -458,7 +416,7 @@ const thebe_selector_output = ".output, .cell_output"
         aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
     <div class="dropdown-buttons">
         
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/hmm.ipynb"><button type="button"
+        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/hmm/hmm.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
                 data-placement="left"><img class="binder-button-logo"
                     src="../../_static/images/logo_binder.svg"
@@ -466,7 +424,7 @@ const thebe_selector_output = ".output, .cell_output"
         
         
         
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/hmm.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
+        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/hmm/hmm.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
                 title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
                     src="../../_static/images/logo_colab.png"
                     alt="Interact on Colab">Colab</button></a>
@@ -688,7 +646,7 @@ const thebe_selector_output = ".output, .cell_output"
 <p>We first create the “Ocassionally dishonest casino” model from <span id="id1">[<a class="reference internal" href="../../bib.html#id3" title="R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.">DEKM98</a>]</span>.</p>
 <div class="figure align-default" id="casino-fig">
 <a class="reference internal image-reference" href="../../_images/casino.png"><img alt="../../_images/casino.png" src="../../_images/casino.png" style="width: 208.5px; height: 142.5px;" /></a>
-<p class="caption"><span class="caption-number">Fig. 3 </span><span class="caption-text">Illustration of the casino HMM.</span><a class="headerlink" href="#casino-fig" title="Permalink to this image">¶</a></p>
+<p class="caption"><span class="caption-number">Fig. 5 </span><span class="caption-text">Illustration of the casino HMM.</span><a class="headerlink" href="#casino-fig" title="Permalink to this image">¶</a></p>
 </div>
 <p>There are 2 hidden states, each of which emit 6 possible observations.</p>
 <div class="cell docutils container">
@@ -987,7 +945,7 @@ A[i,j] transition probabilites.</p>
         },
         kernelOptions: {
             kernelName: "python3",
-            path: "./chapters/ssm"
+            path: "./chapters/hmm"
         },
         predefinedOutput: true
     }
@@ -999,17 +957,17 @@ A[i,j] transition probabilites.</p>
             
                 <!-- Previous / next buttons -->
 <div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="ssm_index.html" title="previous page">
+    <a class='left-prev' id="prev-link" href="hmm_index.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
             <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Introduction</p>
+            <p class="prev-next-title">Inference in discrete SSMs</p>
         </div>
     </a>
-    <a class='right-next' id="next-link" href="hsmm.html" title="next page">
+    <a class='right-next' id="next-link" href="hmm_filter.html" title="next page">
     <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Hidden Semi-Markov Models</p>
+        <p class="prev-next-title">HMM filtering (forwards algorithm)</p>
     </div>
     <i class="fas fa-angle-right"></i>
     </a>

_build/html/chapters/hmm/hmm_filter.html

@@ -54,7 +54,7 @@ const thebe_selector_output = ".output, .cell_output"
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
     <link rel="next" title="HMM smoothing (forwards-backwards algorithm)" href="hmm_smoother.html" />
-    <link rel="prev" title="Inference in discrete SSMs" href="hmm_index.html" />
+    <link rel="prev" title="Hidden Markov Models" href="hmm.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
     
@@ -99,68 +99,26 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="reference internal" href="hmm_index.html">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul class="current">
+   <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
    <li class="toctree-l2 current active">
     <a class="current reference internal" href="#">
      HMM filtering (forwards algorithm)
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -527,11 +485,11 @@ const thebe_selector_output = ".output, .cell_output"
             
                 <!-- Previous / next buttons -->
 <div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="hmm_index.html" title="previous page">
+    <a class='left-prev' id="prev-link" href="hmm.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
             <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Inference in discrete SSMs</p>
+            <p class="prev-next-title">Hidden Markov Models</p>
         </div>
     </a>
     <a class='right-next' id="next-link" href="hmm_smoother.html" title="next page">

_build/html/chapters/hmm/hmm_index.html

@@ -53,8 +53,8 @@ const thebe_selector_output = ".output, .cell_output"
     <script async="async" src="../../_static/sphinx-thebe.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="HMM filtering (forwards algorithm)" href="hmm_filter.html" />
-    <link rel="prev" title="Recurrent Neural Networks" href="../ssm/rnn.html" />
+    <link rel="next" title="Hidden Markov Models" href="hmm.html" />
+    <link rel="prev" title="What are State Space Models?" href="../ssm/ssm.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
     
@@ -99,69 +99,27 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   What are State Space Models?
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="current reference internal" href="#">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul>
    <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
+   <li class="toctree-l2">
     <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -481,6 +439,7 @@ const thebe_selector_output = ".output, .cell_output"
 <p>This chapter covers inference in HMMs.</p>
 <div class="toctree-wrapper compound">
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="hmm.html">Hidden Markov Models</a></li>
 <li class="toctree-l1"><a class="reference internal" href="hmm_filter.html">HMM filtering (forwards algorithm)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="hmm_smoother.html">HMM smoothing (forwards-backwards algorithm)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="hmm_viterbi.html">Viterbi algorithm</a></li>
@@ -516,17 +475,17 @@ const thebe_selector_output = ".output, .cell_output"
             
                 <!-- Previous / next buttons -->
 <div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="../ssm/rnn.html" title="previous page">
+    <a class='left-prev' id="prev-link" href="../ssm/ssm.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
             <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Recurrent Neural Networks</p>
+            <p class="prev-next-title">What are State Space Models?</p>
         </div>
     </a>
-    <a class='right-next' id="next-link" href="hmm_filter.html" title="next page">
+    <a class='right-next' id="next-link" href="hmm.html" title="next page">
     <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">HMM filtering (forwards algorithm)</p>
+        <p class="prev-next-title">Hidden Markov Models</p>
     </div>
     <i class="fas fa-angle-right"></i>
     </a>

_build/html/chapters/hmm/hmm_parallel.html

@@ -99,69 +99,27 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="reference internal" href="hmm_index.html">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul class="current">
    <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
+   <li class="toctree-l2">
     <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/hmm/hmm_sampling.html

@@ -99,69 +99,27 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="reference internal" href="hmm_index.html">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul class="current">
    <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
+   <li class="toctree-l2">
     <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/hmm/hmm_smoother.html

@@ -99,69 +99,27 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="reference internal" href="hmm_index.html">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul class="current">
    <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
+   <li class="toctree-l2">
     <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/hmm/hmm_viterbi.html

@@ -99,69 +99,27 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
  </li>
  <li class="toctree-l1 current active has-children">
   <a class="reference internal" href="hmm_index.html">
    Inference in discrete SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
    <i class="fas fa-chevron-down">
    </i>
   </label>
   <ul class="current">
    <li class="toctree-l2">
+    <a class="reference internal" href="hmm.html">
+     Hidden Markov Models
+    </a>
+   </li>
+   <li class="toctree-l2">
     <a class="reference internal" href="hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/learning/em.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/learning/learning_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="current reference internal" href="#">
    Offline parameter estimation (learning)
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/learning/mcmc.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/learning/sgd.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/learning/vb.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/lgssm/kalman_filter.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/lgssm/kalman_parallel.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/lgssm/kalman_sampling.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/lgssm/kalman_smoother.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/lgssm/lgssm_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="current reference internal" href="#">
    Inference in linear-Gaussian SSMs
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/ode/ode_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/pf/pf_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/postlin/postlin_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/quadrature/quadrature_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/scratch.html

@@ -55,7 +55,7 @@ const thebe_selector_output = ".output, .cell_output"
     <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Introduction" href="ssm/ssm_index.html" />
+    <link rel="next" title="Boilerplate" href="ssm/ssm.html" />
     <link rel="prev" title="State Space Models: A Modern Approach" href="../root.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
@@ -101,9 +101,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -112,58 +117,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="ssm/hmm.html">
+    <a class="reference internal" href="hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -194,8 +152,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -226,8 +184,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -253,8 +211,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -305,8 +263,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -684,10 +642,10 @@ In <a class="reference internal" href="#cat-dog2"><span class="std std-numref">F
             <p class="prev-next-title">State Space Models: A Modern Approach</p>
         </div>
     </a>
-    <a class='right-next' id="next-link" href="ssm/ssm_index.html" title="next page">
+    <a class='right-next' id="next-link" href="ssm/ssm.html" title="next page">
     <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Introduction</p>
+        <p class="prev-next-title">Boilerplate</p>
     </div>
     <i class="fas fa-angle-right"></i>
     </a>

_build/html/chapters/smc/smc_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/ssm/deep.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Deep SSMs &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Recurrent Neural Networks" href="rnn.html" />
-    <link rel="prev" title="Switching SSMs" href="switching.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/deep.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/deep.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/deep.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/deep.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Deep SSMs</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="deep-ssms">
-<h1>Deep SSMs<a class="headerlink" href="#deep-ssms" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="switching.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Switching SSMs</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="rnn.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Recurrent Neural Networks</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/hsmm.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Hidden Semi-Markov Models &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Linear Gaussian SSMs" href="lgssm.html" />
-    <link rel="prev" title="Hidden Markov Models" href="hmm.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/hsmm.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/hsmm.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/hsmm.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/hsmm.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Hidden Semi-Markov Models</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="hidden-semi-markov-models">
-<h1>Hidden Semi-Markov Models<a class="headerlink" href="#hidden-semi-markov-models" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="hmm.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Hidden Markov Models</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="lgssm.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Linear Gaussian SSMs</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/lgssm.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Linear Gaussian SSMs &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Non-Linear Gaussian SSMs" href="nonlin.html" />
-    <link rel="prev" title="Hidden Semi-Markov Models" href="hsmm.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/lgssm.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/lgssm.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/lgssm.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/lgssm.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Linear Gaussian SSMs</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="linear-gaussian-ssms">
-<h1>Linear Gaussian SSMs<a class="headerlink" href="#linear-gaussian-ssms" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="hsmm.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Hidden Semi-Markov Models</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="nonlin.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Non-Linear Gaussian SSMs</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/nongauss.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Non-Gaussian SSMs &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Switching SSMs" href="switching.html" />
-    <link rel="prev" title="Non-Linear Gaussian SSMs" href="nonlin.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/nongauss.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/nongauss.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/nongauss.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/nongauss.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Non-Gaussian SSMs</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="non-gaussian-ssms">
-<h1>Non-Gaussian SSMs<a class="headerlink" href="#non-gaussian-ssms" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="nonlin.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Non-Linear Gaussian SSMs</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="switching.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Switching SSMs</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/nonlin.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Non-Linear Gaussian SSMs &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Non-Gaussian SSMs" href="nongauss.html" />
-    <link rel="prev" title="Linear Gaussian SSMs" href="lgssm.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/nonlin.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/nonlin.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/nonlin.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/nonlin.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Non-Linear Gaussian SSMs</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="non-linear-gaussian-ssms">
-<h1>Non-Linear Gaussian SSMs<a class="headerlink" href="#non-linear-gaussian-ssms" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="lgssm.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Linear Gaussian SSMs</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="nongauss.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Non-Gaussian SSMs</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/rnn.html

@@ -1,565 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Recurrent Neural Networks &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Inference in discrete SSMs" href="../hmm/hmm_index.html" />
-    <link rel="prev" title="Deep SSMs" href="deep.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="reference internal" href="ssm_index.html">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul class="current">
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2 current active">
-    <a class="current reference internal" href="#">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/rnn.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.ipynb</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/rnn.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
-    <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/ssm-jax/ssm-book/main?urlpath=tree/chapters/ssm/rnn.ipynb"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
-                data-placement="left"><img class="binder-button-logo"
-                    src="../../_static/images/logo_binder.svg"
-                    alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/ssm-jax/ssm-book/blob/main/chapters/ssm/rnn.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
-                title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
-                    src="../../_static/images/logo_colab.png"
-                    alt="Interact on Colab">Colab</button></a>
-        
-        
-    </div>
-</div>
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Recurrent Neural Networks</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="recurrent-neural-networks">
-<h1>Recurrent Neural Networks<a class="headerlink" href="#recurrent-neural-networks" title="Permalink to this headline">¶</a></h1>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="deep.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Deep SSMs</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="../hmm/hmm_index.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Inference in discrete SSMs</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/ssm/ssm_index.html

@@ -1,555 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Introduction &#8212; State Space Models: A Modern Approach</title>
-    
-  <link href="../../_static/css/theme.css" rel="stylesheet">
-  <link href="../../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    
-      
-
-    
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
-    <link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/mystnb.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
-  <link rel="preload" as="script" href="../../_static/js/index.be7d3bbb2ef33a8344ce.js">
-
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/clipboard.min.js"></script>
-    <script src="../../_static/copybutton.js"></script>
-    <script>let toggleHintShow = 'Click to show';</script>
-    <script>let toggleHintHide = 'Click to hide';</script>
-    <script>let toggleOpenOnPrint = 'true';</script>
-    <script src="../../_static/togglebutton.js"></script>
-    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
-    <script src="../../_static/sphinx-book-theme.d59cb220de22ca1c485ebbdc042f0030.js"></script>
-    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
-const thebe_selector = ".thebe,.cell"
-const thebe_selector_input = "pre"
-const thebe_selector_output = ".output, .cell_output"
-</script>
-    <script async="async" src="../../_static/sphinx-thebe.js"></script>
-    <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Hidden Markov Models" href="hmm.html" />
-    <link rel="prev" title="Scratchpad" href="../scratch.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
-
-    <!-- Google Analytics -->
-    
-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
-    <div class="container-fluid" id="banner"></div>
-
-    
-
-    <div class="container-xl">
-      <div class="row">
-          
-<div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
-        <div class="navbar-brand-box">
-    <a class="navbar-brand text-wrap" href="../../index.html">
-      
-      
-      
-      <h1 class="site-logo" id="site-title">State Space Models: A Modern Approach</h1>
-      
-    </a>
-</div><form class="bd-search d-flex align-items-center" action="../../search.html" method="get">
-  <i class="icon fas fa-search"></i>
-  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
-</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
-    <div class="bd-toc-item active">
-        <ul class="nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../../root.html">
-   State Space Models: A Modern Approach
-  </a>
- </li>
-</ul>
-<ul class="current nav bd-sidenav">
- <li class="toctree-l1">
-  <a class="reference internal" href="../scratch.html">
-   Scratchpad
-  </a>
- </li>
- <li class="toctree-l1 current active has-children">
-  <a class="current reference internal" href="#">
-   Introduction
-  </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
-  <label for="toctree-checkbox-1">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hmm.html">
-     Hidden Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_filter.html">
-     HMM filtering (forwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_smoother.html">
-     HMM smoothing (forwards-backwards algorithm)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_viterbi.html">
-     Viterbi algorithm
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_parallel.html">
-     Parallel HMM  smoothing
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../hmm/hmm_sampling.html">
-     Forwards-filtering backwards-sampling algorithm
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../lgssm/lgssm_index.html">
-   Inference in linear-Gaussian SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_filter.html">
-     Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_smoother.html">
-     Kalman (RTS) smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_parallel.html">
-     Parallel Kalman Smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../lgssm/kalman_sampling.html">
-     Forwards-filtering backwards sampling
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../extended/extended_index.html">
-   Extended (linearized) methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_filter.html">
-     Extended Kalman filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_smoother.html">
-     Extended Kalman smoother
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../extended/extended_parallel.html">
-     Parallel extended Kalman smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../unscented/unscented_index.html">
-   Unscented methods
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_filter.html">
-     Unscented filtering
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../unscented/unscented_smoother.html">
-     Unscented smoothing
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../quadrature/quadrature_index.html">
-   Quadrature and cubature methods
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../postlin/postlin_index.html">
-   Posterior linearization
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../adf/adf_index.html">
-   Assumed Density Filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../vi/vi_index.html">
-   Variational inference
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../pf/pf_index.html">
-   Particle filtering
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../smc/smc_index.html">
-   Sequential Monte Carlo
-  </a>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../learning/learning_index.html">
-   Offline parameter estimation (learning)
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/em.html">
-     Expectation Maximization (EM)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/sgd.html">
-     Stochastic Gradient Descent (SGD)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/vb.html">
-     Variational Bayes (VB)
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../learning/mcmc.html">
-     Markov Chain Monte Carlo (MCMC)
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../tracking/tracking_index.html">
-   Multi-target tracking
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ensemble/ensemble_index.html">
-   Data assimilation using Ensemble Kalman filter
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../bnp/bnp_index.html">
-   Bayesian non-parametric SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../changepoint/changepoint_index.html">
-   Changepoint detection
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../timeseries/timeseries_index.html">
-   Timeseries forecasting
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../gp/gp_index.html">
-   Markovian Gaussian processes
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../ode/ode_index.html">
-   Differential equations and SSMs
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../control/control_index.html">
-   Optimal control
-  </a>
- </li>
- <li class="toctree-l1">
-  <a class="reference internal" href="../../bib.html">
-   Bibliography
-  </a>
- </li>
-</ul>
-
-    </div>
-</nav> <!-- To handle the deprecated key -->
-
-<div class="navbar_extra_footer">
-  Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
-</div>
-
-</div>
-
-
-          
-
-
-          
-<main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
-    <div class="topbar container-xl fixed-top">
-    <div class="topbar-contents row">
-        <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
-        <div class="col pl-md-4 topbar-main">
-            
-            <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
-                data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
-                aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
-                title="Toggle navigation" data-toggle="tooltip" data-placement="left">
-                <i class="fas fa-bars"></i>
-                <i class="fas fa-arrow-left"></i>
-                <i class="fas fa-arrow-up"></i>
-            </button>
-            
-            
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
-            class="fas fa-download"></i></button>
-
-    <div class="dropdown-buttons">
-        <!-- ipynb file if we had a myst markdown file -->
-        
-        <!-- Download raw file -->
-        <a class="dropdown-buttons" href="../../_sources/chapters/ssm/ssm_index.md"><button type="button"
-                class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
-                data-placement="left">.md</button></a>
-        <!-- Download PDF via print -->
-        <button type="button" id="download-print" class="btn btn-secondary topbarbtn" title="Print to PDF"
-                onclick="printPdf(this)" data-toggle="tooltip" data-placement="left">.pdf</button>
-    </div>
-</div>
-
-            <!-- Source interaction buttons -->
-
-<div class="dropdown-buttons-trigger">
-    <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
-        aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
-    <div class="dropdown-buttons sourcebuttons">
-        <a class="repository-button"
-            href="https://github.com/ssm-jax/ssm-book"><button type="button" class="btn btn-secondary topbarbtn"
-                data-toggle="tooltip" data-placement="left" title="Source repository"><i
-                    class="fab fa-github"></i>repository</button></a>
-        <a class="issues-button"
-            href="https://github.com/ssm-jax/ssm-book/issues/new?title=Issue%20on%20page%20%2Fchapters/ssm/ssm_index.html&body=Your%20issue%20content%20here."><button
-                type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
-                title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
-    </div>
-</div>
-
-            <!-- Full screen (wrap in <a> to have style consistency -->
-
-<a class="full-screen-button"><button type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip"
-        data-placement="bottom" onclick="toggleFullScreen()" aria-label="Fullscreen mode"
-        title="Fullscreen mode"><i
-            class="fas fa-expand"></i></button></a>
-
-            <!-- Launch buttons -->
-
-        </div>
-
-        <!-- Table of contents -->
-        <div class="d-none d-md-block col-md-2 bd-toc show noprint">
-            
-        </div>
-    </div>
-</div>
-    <div id="main-content" class="row">
-        <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-            <!-- Table of contents that is only displayed when printing the page -->
-            <div id="jb-print-docs-body" class="onlyprint">
-                <h1>Introduction</h1>
-                <!-- Table of contents -->
-                <div id="print-main-content">
-                    <div id="jb-print-toc">
-                        
-                    </div>
-                </div>
-            </div>
-            
-              <div>
-                
-  <div class="tex2jax_ignore mathjax_ignore section" id="introduction">
-<span id="ch-ssm"></span><h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="hmm.html">Hidden Markov Models</a></li>
-<li class="toctree-l1"><a class="reference internal" href="hsmm.html">Hidden Semi-Markov Models</a></li>
-<li class="toctree-l1"><a class="reference internal" href="lgssm.html">Linear Gaussian SSMs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="nonlin.html">Non-Linear Gaussian SSMs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="nongauss.html">Non-Gaussian SSMs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="switching.html">Switching SSMs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="deep.html">Deep SSMs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="rnn.html">Recurrent Neural Networks</a></li>
-</ul>
-</div>
-</div>
-
-    <script type="text/x-thebe-config">
-    {
-        requestKernel: true,
-        binderOptions: {
-            repo: "binder-examples/jupyter-stacks-datascience",
-            ref: "master",
-        },
-        codeMirrorConfig: {
-            theme: "abcdef",
-            mode: "python"
-        },
-        kernelOptions: {
-            kernelName: "python3",
-            path: "./chapters/ssm"
-        },
-        predefinedOutput: true
-    }
-    </script>
-    <script>kernelName = 'python3'</script>
-
-              </div>
-              
-            
-                <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
-    <a class='left-prev' id="prev-link" href="../scratch.html" title="previous page">
-        <i class="fas fa-angle-left"></i>
-        <div class="prev-next-info">
-            <p class="prev-next-subtitle">previous</p>
-            <p class="prev-next-title">Scratchpad</p>
-        </div>
-    </a>
-    <a class='right-next' id="next-link" href="hmm.html" title="next page">
-    <div class="prev-next-info">
-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Hidden Markov Models</p>
-    </div>
-    <i class="fas fa-angle-right"></i>
-    </a>
-</div>
-            
-        </div>
-    </div>
-    <footer class="footer">
-  <p>
-    
-      By Kevin Murphy, Scott Linderman, et al.<br/>
-    
-        &copy; Copyright 2021.<br/>
-  </p>
-</footer>
-</main>
-
-
-      </div>
-    </div>
-  
-  <script src="../../_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-
-  </body>
-</html>

_build/html/chapters/timeseries/timeseries_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/tracking/tracking_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/unscented/unscented_filter.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="unscented_index.html">
    Unscented methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/unscented/unscented_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="current reference internal" href="#">
    Unscented methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/unscented/unscented_smoother.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="unscented_index.html">
    Unscented methods
   </a>
-  <input checked="" class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input checked="" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/chapters/vi/vi_index.html

@@ -99,9 +99,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ssm/ssm.html">
+   Boilerplate
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="../hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -110,58 +115,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hmm.html">
+    <a class="reference internal" href="../hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="../ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="../hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="../hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -192,8 +150,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -224,8 +182,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -251,8 +209,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -303,8 +261,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="../learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/genindex.html

@@ -97,9 +97,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="chapters/ssm/ssm.html">
+   What are State Space Models?
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="chapters/hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -108,58 +113,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hmm.html">
+    <a class="reference internal" href="chapters/hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="chapters/hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -190,8 +148,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -222,8 +180,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -249,8 +207,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -301,8 +259,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/html/reports/ssm.log

@@ -0,0 +1,51 @@
+Traceback (most recent call last):
+  File "/opt/anaconda3/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 1087, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
+    return loop.run_until_complete(coro)
+  File "/opt/anaconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
+    return future.result()
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 540, in async_execute
+    await self.async_execute_cell(
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 832, in async_execute_cell
+    self._check_raise_for_error(cell, exec_reply)
+  File "/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 740, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+# state transition matrix
+A = np.array([
+    [0.95, 0.05],
+    [0.10, 0.90]
+])
+
+# observation matrix
+B = np.array([
+    [1/6, 1/6, 1/6, 1/6, 1/6, 1/6], # fair die
+    [1/10, 1/10, 1/10, 1/10, 1/10, 5/10] # loaded die
+])
+
+pi, _ = normalize(np.array([1, 1]))
+pi = np.array(pi)
+
+
+(nstates, nobs) = np.shape(B)
+
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+<ipython-input-3-2f308bef5393> in <module>
+     11 ])
+     12 
+---> 13 pi, _ = normalize(np.array([1, 1]))
+     14 pi = np.array(pi)
+     15 
+
+NameError: name 'normalize' is not defined
+NameError: name 'normalize' is not defined
+

_build/html/root.html

@@ -98,9 +98,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="chapters/ssm/ssm.html">
+   What are State Space Models?
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="chapters/hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -109,58 +114,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hmm.html">
+    <a class="reference internal" href="chapters/hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="chapters/hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -191,8 +149,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -223,8 +181,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -250,8 +208,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -302,8 +260,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -488,18 +446,9 @@ in automatic differentiation and parallel computing.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="chapters/scratch.html">Scratchpad</a></li>
-<li class="toctree-l1"><a class="reference internal" href="chapters/ssm/ssm_index.html">Introduction</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/hmm.html">Hidden Markov Models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/hsmm.html">Hidden Semi-Markov Models</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/lgssm.html">Linear Gaussian SSMs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/nonlin.html">Non-Linear Gaussian SSMs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/nongauss.html">Non-Gaussian SSMs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/switching.html">Switching SSMs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/deep.html">Deep SSMs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="chapters/ssm/rnn.html">Recurrent Neural Networks</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="chapters/ssm/ssm.html">What are State Space Models?</a></li>
 <li class="toctree-l1"><a class="reference internal" href="chapters/hmm/hmm_index.html">Inference in discrete SSMs</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="chapters/hmm/hmm.html">Hidden Markov Models</a></li>
 <li class="toctree-l2"><a class="reference internal" href="chapters/hmm/hmm_filter.html">HMM filtering (forwards algorithm)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="chapters/hmm/hmm_smoother.html">HMM smoothing (forwards-backwards algorithm)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="chapters/hmm/hmm_viterbi.html">Viterbi algorithm</a></li>

_build/html/search.html

@@ -103,9 +103,14 @@ const thebe_selector_output = ".output, .cell_output"
    Scratchpad
   </a>
  </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="chapters/ssm/ssm.html">
+   What are State Space Models?
+  </a>
+ </li>
  <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/ssm/ssm_index.html">
-   Introduction
+  <a class="reference internal" href="chapters/hmm/hmm_index.html">
+   Inference in discrete SSMs
   </a>
   <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
   <label for="toctree-checkbox-1">
@@ -114,58 +119,11 @@ const thebe_selector_output = ".output, .cell_output"
   </label>
   <ul>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hmm.html">
+    <a class="reference internal" href="chapters/hmm/hmm.html">
      Hidden Markov Models
     </a>
    </li>
    <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/hsmm.html">
-     Hidden Semi-Markov Models
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/lgssm.html">
-     Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nonlin.html">
-     Non-Linear Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/nongauss.html">
-     Non-Gaussian SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/switching.html">
-     Switching SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/deep.html">
-     Deep SSMs
-    </a>
-   </li>
-   <li class="toctree-l2">
-    <a class="reference internal" href="chapters/ssm/rnn.html">
-     Recurrent Neural Networks
-    </a>
-   </li>
-  </ul>
- </li>
- <li class="toctree-l1 has-children">
-  <a class="reference internal" href="chapters/hmm/hmm_index.html">
-   Inference in discrete SSMs
-  </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
-  <label for="toctree-checkbox-2">
-   <i class="fas fa-chevron-down">
-   </i>
-  </label>
-  <ul>
-   <li class="toctree-l2">
     <a class="reference internal" href="chapters/hmm/hmm_filter.html">
      HMM filtering (forwards algorithm)
     </a>
@@ -196,8 +154,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/lgssm/lgssm_index.html">
    Inference in linear-Gaussian SSMs
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
-  <label for="toctree-checkbox-3">
+  <input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
+  <label for="toctree-checkbox-2">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -228,8 +186,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/extended/extended_index.html">
    Extended (linearized) methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
-  <label for="toctree-checkbox-4">
+  <input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/>
+  <label for="toctree-checkbox-3">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -255,8 +213,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/unscented/unscented_index.html">
    Unscented methods
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
-  <label for="toctree-checkbox-5">
+  <input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" type="checkbox"/>
+  <label for="toctree-checkbox-4">
    <i class="fas fa-chevron-down">
    </i>
   </label>
@@ -307,8 +265,8 @@ const thebe_selector_output = ".output, .cell_output"
   <a class="reference internal" href="chapters/learning/learning_index.html">
    Offline parameter estimation (learning)
   </a>
-  <input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/>
-  <label for="toctree-checkbox-6">
+  <input class="toctree-checkbox" id="toctree-checkbox-5" name="toctree-checkbox-5" type="checkbox"/>
+  <label for="toctree-checkbox-5">
    <i class="fas fa-chevron-down">
    </i>
   </label>

_build/jupyter_execute/chapters/learning/em.ipynb

@@ -27,7 +27,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

_build/jupyter_execute/chapters/learning/mcmc.ipynb

@@ -26,7 +26,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

_build/jupyter_execute/chapters/learning/sgd.ipynb

@@ -26,7 +26,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

_build/jupyter_execute/chapters/learning/vb.ipynb

@@ -27,7 +27,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

_build/jupyter_execute/chapters/scratch.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "8effb7c4",
+   "id": "6986d0f3",
    "metadata": {},
    "source": [
     "(ch:intro)=\n",
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "a9311a84",
+   "id": "5d887c30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "41386a79",
+   "id": "57031b40",
    "metadata": {},
    "outputs": [
     {
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "55b29f42",
+   "id": "5e9e11d3",
    "metadata": {},
    "outputs": [
     {
@@ -113,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6c78ea7d",
+   "id": "264fb6e0",
    "metadata": {},
    "source": [
     "## Images\n",

_build/jupyter_execute/chapters/ssm/deep.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Deep SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/jupyter_execute/chapters/ssm/deep.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# # Deep SSMs
-# 
-
-# 

_build/jupyter_execute/chapters/ssm/hsmm.ipynb

@@ -1,33 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Hidden Semi-Markov Models\n",
-    "\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/jupyter_execute/chapters/ssm/hsmm.py

@@ -1,6 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# # Hidden Semi-Markov Models
-# 
-# 

_build/jupyter_execute/chapters/ssm/lgssm.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Linear Gaussian SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/jupyter_execute/chapters/ssm/lgssm.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# # Linear Gaussian SSMs
-# 
-
-# 

_build/jupyter_execute/chapters/ssm/nongauss.ipynb

@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#  Non-Gaussian SSMs\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/jupyter_execute/chapters/ssm/nongauss.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# #  Non-Gaussian SSMs
-# 
-
-# 

_build/jupyter_execute/chapters/ssm/nonlin.ipynb

@@ -1,32 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Non-Linear Gaussian SSMs\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

_build/jupyter_execute/chapters/ssm/nonlin.py

@@ -1,5 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-# # Non-Linear Gaussian SSMs
-#