update docs (#155)

update docs
oturns · Oct 31, 2019 · 09daae3 · 09daae3
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <h1 align="center"><code>geosnap</code></h1>
 <p align="center">
-<img height=100  src="docs/geosnap.png" alt="geosnap"/>
+<img height=100  src="docs/figs/geosnap.svg" alt="geosnap"/>
 </p>
 <h2 align="center" style="margin-top:-10px">The GeoSpatial Neighborhood Analysis Package</h2> 
 
@@ -224,6 +224,7 @@ classic clustering methods on the `Community`
 dc.cluster(method='kmeans', n_clusters=6, columns=['p_unemployment_rate', 'per_capita_income'] )
 dc.gdf[dc.gdf.year==2000].plot(column='kmeans')
 ```
+
 <p align="center">
 <img height=250 src="docs/figs/output_6_1.png"/>
 </p>
@@ -236,6 +237,7 @@ spatially-constrained clustering methods on the `Community`
 dc.cluster_spatial(method='spenc', n_clusters=6, columns=['p_unemployment_rate', 'per_capita_income'] )
 dc.gdf[dc.gdf.year==2000].plot('spenc')
 ```
+
 <p align="center">
 <img height=250 src="docs/figs/output_9_1.png"/>
 </p>

diff --git a/docs/.nojekyll b/docs/.nojekyll
@@ -1 +0,0 @@
-

diff --git a/docs/_modules/geosnap/analyze/analytics.html b/docs/_modules/geosnap/analyze/analytics.html
@@ -137,7 +137,7 @@ <h1>Source code for geosnap.analyze.analytics</h1><div class="highlight"><pre>
 <span class="p">)</span>
 
 
-<div class="viewcode-block" id="cluster"><a class="viewcode-back" href="../../../generated/osnap.analyze.cluster.html#geosnap.analyze.cluster">[docs]</a><span class="k">def</span> <span class="nf">cluster</span><span class="p">(</span>
+<div class="viewcode-block" id="cluster"><a class="viewcode-back" href="../../../generated/geosnap.analyze.analytics.html#geosnap.analyze.cluster">[docs]</a><span class="k">def</span> <span class="nf">cluster</span><span class="p">(</span>
     <span class="n">gdf</span><span class="p">,</span>
     <span class="n">n_clusters</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span>
     <span class="n">method</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -229,7 +229,7 @@ <h1>Source code for geosnap.analyze.analytics</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">gdf</span></div>
 
 
-<div class="viewcode-block" id="cluster_spatial"><a class="viewcode-back" href="../../../generated/osnap.analyze.cluster_spatial.html#geosnap.analyze.cluster_spatial">[docs]</a><span class="k">def</span> <span class="nf">cluster_spatial</span><span class="p">(</span>
+<div class="viewcode-block" id="cluster_spatial"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster_spatial.html#geosnap.analyze.cluster_spatial">[docs]</a><span class="k">def</span> <span class="nf">cluster_spatial</span><span class="p">(</span>
     <span class="n">gdf</span><span class="p">,</span>
     <span class="n">n_clusters</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span>
     <span class="n">spatial_weights</span><span class="o">=</span><span class="s2">&quot;rook&quot;</span><span class="p">,</span>

diff --git a/docs/_modules/geosnap/analyze/cluster.html b/docs/_modules/geosnap/analyze/cluster.html
@@ -132,7 +132,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
 <span class="c1"># Sklearn a-spatial models</span>
 
 
-<div class="viewcode-block" id="ward"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.ward.html#geosnap.analyze.analytics.ward">[docs]</a><span class="k">def</span> <span class="nf">ward</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="ward"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.ward">[docs]</a><span class="k">def</span> <span class="nf">ward</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Agglomerative clustering using Ward linkage.</span>
 
 <span class="sd">    Parameters</span>
@@ -154,7 +154,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="kmeans"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.kmeans.html#geosnap.analyze.analytics.kmeans">[docs]</a><span class="k">def</span> <span class="nf">kmeans</span><span class="p">(</span>
+<div class="viewcode-block" id="kmeans"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.kmeans">[docs]</a><span class="k">def</span> <span class="nf">kmeans</span><span class="p">(</span>
     <span class="n">X</span><span class="p">,</span>
     <span class="n">n_clusters</span><span class="p">,</span>
     <span class="n">init</span><span class="o">=</span><span class="s2">&quot;k-means++&quot;</span><span class="p">,</span>
@@ -214,7 +214,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="affinity_propagation"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.affinity_propagation.html#geosnap.analyze.analytics.affinity_propagation">[docs]</a><span class="k">def</span> <span class="nf">affinity_propagation</span><span class="p">(</span>
+<div class="viewcode-block" id="affinity_propagation"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.affinity_propagation">[docs]</a><span class="k">def</span> <span class="nf">affinity_propagation</span><span class="p">(</span>
     <span class="n">X</span><span class="p">,</span>
     <span class="n">damping</span><span class="o">=</span><span class="mf">0.8</span><span class="p">,</span>
     <span class="n">preference</span><span class="o">=-</span><span class="mi">1000</span><span class="p">,</span>
@@ -263,7 +263,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="spectral"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.spectral.html#geosnap.analyze.analytics.spectral">[docs]</a><span class="k">def</span> <span class="nf">spectral</span><span class="p">(</span>
+<div class="viewcode-block" id="spectral"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.spectral">[docs]</a><span class="k">def</span> <span class="nf">spectral</span><span class="p">(</span>
     <span class="n">X</span><span class="p">,</span>
     <span class="n">n_clusters</span><span class="p">,</span>
     <span class="n">eigen_solver</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -340,7 +340,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="gaussian_mixture"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.gaussian_mixture.html#geosnap.analyze.analytics.gaussian_mixture">[docs]</a><span class="k">def</span> <span class="nf">gaussian_mixture</span><span class="p">(</span>
+<div class="viewcode-block" id="gaussian_mixture"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.gaussian_mixture">[docs]</a><span class="k">def</span> <span class="nf">gaussian_mixture</span><span class="p">(</span>
     <span class="n">X</span><span class="p">,</span>
     <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
     <span class="n">covariance_type</span><span class="o">=</span><span class="s2">&quot;full&quot;</span><span class="p">,</span>
@@ -425,7 +425,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="hdbscan"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.hdbscan.html#geosnap.analyze.analytics.hdbscan">[docs]</a><span class="k">def</span> <span class="nf">hdbscan</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">min_cluster_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">gen_min_span_tree</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="hdbscan"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.hdbscan">[docs]</a><span class="k">def</span> <span class="nf">hdbscan</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">min_cluster_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">gen_min_span_tree</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Clustering with Hierarchical DBSCAN</span>
 
 <span class="sd">    Parameters</span>
@@ -459,7 +459,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
 <span class="c1"># Spatially Explicit/Encouraged Methods</span>
 
 
-<div class="viewcode-block" id="ward_spatial"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.ward_spatial.html#geosnap.analyze.analytics.ward_spatial">[docs]</a><span class="k">def</span> <span class="nf">ward_spatial</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="ward_spatial"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.ward_spatial">[docs]</a><span class="k">def</span> <span class="nf">ward_spatial</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Agglomerative clustering using Ward linkage with a spatial connectivity</span>
 <span class="sd">       constraint</span>
 
@@ -488,7 +488,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="spenc"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.spenc.html#geosnap.analyze.analytics.spenc">[docs]</a><span class="k">def</span> <span class="nf">spenc</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">gamma</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="spenc"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.spenc">[docs]</a><span class="k">def</span> <span class="nf">spenc</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">gamma</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Spatially encouraged spectral clustering</span>
 
 <span class="sd">    :cite:`wolf2018`</span>
@@ -519,7 +519,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="skater"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.skater.html#geosnap.analyze.analytics.skater">[docs]</a><span class="k">def</span> <span class="nf">skater</span><span class="p">(</span>
+<div class="viewcode-block" id="skater"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.skater">[docs]</a><span class="k">def</span> <span class="nf">skater</span><span class="p">(</span>
     <span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">floor</span><span class="o">=-</span><span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">,</span> <span class="n">trace</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">islands</span><span class="o">=</span><span class="s2">&quot;increase&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span>
 <span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;SKATER spatial clustering algorithm.</span>
@@ -558,7 +558,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="azp"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.azp.html#geosnap.analyze.analytics.azp">[docs]</a><span class="k">def</span> <span class="nf">azp</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="azp"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.azp">[docs]</a><span class="k">def</span> <span class="nf">azp</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">n_clusters</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;AZP clustering algorithm</span>
 
 <span class="sd">    Parameters</span>
@@ -584,7 +584,7 @@ <h1>Source code for geosnap.analyze.cluster</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">model</span></div>
 
 
-<div class="viewcode-block" id="max_p"><a class="viewcode-back" href="../../../generated/osnap.analyze.analytics.max_p.html#geosnap.analyze.analytics.max_p">[docs]</a><span class="k">def</span> <span class="nf">max_p</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">threshold_variable</span><span class="o">=</span><span class="s2">&quot;count&quot;</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="max_p"><a class="viewcode-back" href="../../../generated/geosnap.analyze.cluster.html#geosnap.analyze.analytics.max_p">[docs]</a><span class="k">def</span> <span class="nf">max_p</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">w</span><span class="p">,</span> <span class="n">threshold_variable</span><span class="o">=</span><span class="s2">&quot;count&quot;</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Max-p clustering algorithm</span>
 <span class="sd">    :cite:`Duque2012`</span>
 

diff --git a/docs/_modules/geosnap/analyze/incs.html b/docs/_modules/geosnap/analyze/incs.html
@@ -150,7 +150,7 @@ <h1>Source code for geosnap.analyze.incs</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">neighborhoods</span>
 
 
-<div class="viewcode-block" id="linc"><a class="viewcode-back" href="../../../generated/osnap.analyze.linc.html#geosnap.analyze.linc">[docs]</a><span class="k">def</span> <span class="nf">linc</span><span class="p">(</span><span class="n">labels_sequence</span><span class="p">):</span>
+<div class="viewcode-block" id="linc"><a class="viewcode-back" href="../../../generated/geosnap.analyze.linc.html#geosnap.analyze.linc">[docs]</a><span class="k">def</span> <span class="nf">linc</span><span class="p">(</span><span class="n">labels_sequence</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Local Indicator of Neighborhood Change</span>