Update documentation

chapters/hmm/hmm.html

@@ -646,7 +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. 6 </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. 7 </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">

reports/ssm.log

@@ -17,35 +17,23 @@ Traceback (most recent call last):
     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)
+# MAP estimation
+fig, ax = plt.subplots()
+plot_inference(z_map, z_hist, ax, map_estimate=True)
+ax.set_ylabel("MAP state")
+ax.set_title("Viterbi")
 
 ------------------
 
 ---------------------------------------------------------------------------
 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
+<ipython-input-12-d20416120056> in <module>
+      1 # MAP estimation
+      2 fig, ax = plt.subplots()
+----> 3 plot_inference(z_map, z_hist, ax, map_estimate=True)
+      4 ax.set_ylabel("MAP state")
+      5 ax.set_title("Viterbi")
+
+NameError: name 'z_map' is not defined
+NameError: name 'z_map' is not defined
 

root.html

@@ -448,6 +448,8 @@ in automatic differentiation and parallel computing.</p>
 <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.html">What are State Space Models?</a></li>
 <li class="toctree-l1"><a class="reference internal" href="chapters/ssm/ssm.html#hidden-markov-models">Hidden Markov Models</a></li>
+<li class="toctree-l1"><a class="reference internal" href="chapters/ssm/ssm.html#linear-gaussian-ssms">Linear Gaussian SSMs</a></li>
+<li class="toctree-l1"><a class="reference internal" href="chapters/ssm/ssm.html#inferential-goals">Inferential goals</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>