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Native geometries #377

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Jan 12, 2020
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4e1c606
adding snkit reference in spaghetti.Network()
jGaboardi Jan 11, 2020
e6c8365
accepting libpysal.cg.Chain for network instantiation
jGaboardi Jan 11, 2020
b66d067
update Netowrk() docstring
jGaboardi Jan 11, 2020
4131905
adding tests in test_network_api.py
jGaboardi Jan 12, 2020
d4c03ce
adding tests in test_network.py
jGaboardi Jan 12, 2020
fe6881e
1 edge break point in contiguityweights()
jGaboardi Jan 12, 2020
da88794
single chain test for test_network.py
jGaboardi Jan 12, 2020
c5d4539
single chain test for test_network_api.py
jGaboardi Jan 12, 2020
90d77b4
improved TypeError catching
jGaboardi Jan 12, 2020
8b45b69
points testing for test_network.py
jGaboardi Jan 12, 2020
4e80044
points testing for test_network_api.py
jGaboardi Jan 12, 2020
a0cbc3b
adjusting network docstrings
jGaboardi Jan 12, 2020
bfd2d64
adding snkit reference
jGaboardi Jan 12, 2020
337fc0a
pushing updated docs
jGaboardi Jan 12, 2020
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98 changes: 75 additions & 23 deletions docs/_modules/spaghetti/network.html
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10 changes: 10 additions & 0 deletions docs/_static/references.bib
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Expand Up @@ -379,3 +379,13 @@ @article{ReVelle2005
volume = {165},
year = {2005}
}

@misc{tom_russell_2019_3379659,
author = {Tom Russell and Elco Koks},
title = {{tomalrussell/snkit: v1.6.0}},
month = aug,
year = {2019},
publisher = {Zenodo},
version = {v1.6.0},
doi = {10.5281/zenodo.3379659}
}
37 changes: 20 additions & 17 deletions docs/generated/spaghetti.Network.html
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Expand Up @@ -139,8 +139,10 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
<dl class="field-list">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><dl>
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+30.g0da3a7d)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a shapefile
(str); or (2) a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code>.</p>
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">list</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">tuple</span></code></a>, <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.17)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a>, <a class="reference external" href="https://pysal.org/libpysal/generated/libpysal.cg.Chain.html#libpysal.cg.Chain" title="(in libpysal v4.2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">libpysal.cg.Chain</span></code></a>, <a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+33.gadd5fe9)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a shapefile
(str); (2) an iterable containing <code class="docutils literal notranslate"><span class="pre">libpysal.cg.Chain</span></code>
objects; (3) a single <code class="docutils literal notranslate"><span class="pre">libpysal.cg.Chain</span></code>; or
(4) a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code>.</p>
</dd>
<dt><strong>vertex_sig</strong><span class="classifier"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">int</span></code></a></span></dt><dd><p>Round the x and y coordinates of all vertices to <code class="docutils literal notranslate"><span class="pre">vertex_sig</span></code>
significant digits (combined significant digits on the left and
Expand Down Expand Up @@ -171,10 +173,11 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
<a class="bibtex reference internal" href="../references.html#ducruet2014" id="id9">[DB14]</a>, <a class="bibtex reference internal" href="../references.html#weber2016" id="id10">[Web16]</a>, for more in-depth discussion on
spatial networks, graph theory, and location along networks.
For related network-centric software see
<a class="reference external" href="http://sanet.csis.u-tokyo.ac.jp">SANET</a> <a class="bibtex reference internal" href="../references.html#okabe2006a" id="id11">[OOS06]</a>,
<a class="reference external" href="https://networkx.github.io">NetworkX</a> <a class="bibtex reference internal" href="../references.html#hagberg2008" id="id12">[HSS08]</a>,
<a class="reference external" href="http://udst.github.io/pandana/">Pandana</a> <a class="bibtex reference internal" href="../references.html#foti2012" id="id13">[FWL12]</a>,
and <a class="reference external" href="https://osmnx.readthedocs.io/en/stable/">OSMnx</a> <a class="bibtex reference internal" href="../references.html#boeing2017" id="id14">[Boe17]</a>.</p>
<a class="reference external" href="https://github.com/tomalrussell/snkit">Snkit</a> <a class="bibtex reference internal" href="../references.html#tom-russell-2019-3379659" id="id11">[RK19]</a>,
<a class="reference external" href="http://sanet.csis.u-tokyo.ac.jp">SANET</a> <a class="bibtex reference internal" href="../references.html#okabe2006a" id="id12">[OOS06]</a>,
<a class="reference external" href="https://networkx.github.io">NetworkX</a> <a class="bibtex reference internal" href="../references.html#hagberg2008" id="id13">[HSS08]</a>,
<a class="reference external" href="http://udst.github.io/pandana/">Pandana</a> <a class="bibtex reference internal" href="../references.html#foti2012" id="id14">[FWL12]</a>,
and <a class="reference external" href="https://osmnx.readthedocs.io/en/stable/">OSMnx</a> <a class="bibtex reference internal" href="../references.html#boeing2017" id="id15">[Boe17]</a>.</p>
<p class="rubric">Examples</p>
<p>Create an instance of a network.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">spaghetti</span>
Expand Down Expand Up @@ -414,8 +417,8 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1002-9780470549094-ch5" id="id15">[OSullivanU10]</a> and mentioned in
<a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch5" id="id16">[OS12c]</a>.</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1002-9780470549094-ch5" id="id16">[OSullivanU10]</a> and mentioned in
<a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch5" id="id17">[OS12c]</a>.</p>
<p class="rubric">Examples</p>
<p>Create a network instance.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">spaghetti</span>
Expand Down Expand Up @@ -479,8 +482,8 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1002-9780470549094-ch5" id="id17">[OSullivanU10]</a> and mentioned in
<a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch5" id="id18">[OS12c]</a>.</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1002-9780470549094-ch5" id="id18">[OSullivanU10]</a> and mentioned in
<a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch5" id="id19">[OS12c]</a>.</p>
<p>[note from <cite>jlaura</cite>] Both the <cite>G</cite> and <cite>K</cite> functions generate a
full distance matrix. This is because, I know that the full
generation is correct and I believe that the truncated generated,
Expand Down Expand Up @@ -548,8 +551,8 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1111-j-1538-4632-2001-tb00448-x" id="id19">[OY01]</a>
and <a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch6" id="id20">[OS12b]</a>.</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#doi-10-1111-j-1538-4632-2001-tb00448-x" id="id20">[OY01]</a>
and <a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch6" id="id21">[OS12b]</a>.</p>
<p>[note from <cite>jlaura</cite>] Both the <cite>G</cite> and <cite>K</cite> functions generate a
full distance matrix. This is because, I know that the full
generation is correct and I believe that the truncated generated,
Expand Down Expand Up @@ -754,7 +757,7 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>See <a class="bibtex reference internal" href="../references.html#pysal2007" id="id21">[RA07]</a> and <a class="bibtex reference internal" href="../references.html#esda-2019" id="id22">[RWK+19]</a> for more details.</p>
<p>See <a class="bibtex reference internal" href="../references.html#pysal2007" id="id22">[RA07]</a> and <a class="bibtex reference internal" href="../references.html#esda-2019" id="id23">[RWK+19]</a> for more details.</p>
<p class="rubric">Examples</p>
<p>Instantiate a network.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">spaghetti</span>
Expand Down Expand Up @@ -886,7 +889,7 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>See <a class="bibtex reference internal" href="../references.html#anselinrey2014" id="id23">[AR14]</a> and <a class="bibtex reference internal" href="../references.html#rey-open-2015" id="id24">[RAL+15]</a> for more details
<p>See <a class="bibtex reference internal" href="../references.html#anselinrey2014" id="id24">[AR14]</a> and <a class="bibtex reference internal" href="../references.html#rey-open-2015" id="id25">[RAL+15]</a> for more details
regarding spatial weights.</p>
<p class="rubric">Examples</p>
<p>Instantiate an instance of a network.</p>
Expand Down Expand Up @@ -994,7 +997,7 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#dijkstra1959a" id="id25">[Dij59]</a> and <a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch3" id="id26">[OS12a]</a>.</p>
<p>Based on <a class="bibtex reference internal" href="../references.html#dijkstra1959a" id="id26">[Dij59]</a> and <a class="bibtex reference internal" href="../references.html#doi-10-1002-9781119967101-ch3" id="id27">[OS12a]</a>.</p>
</dd></dl>

<dl class="method">
Expand Down Expand Up @@ -1187,7 +1190,7 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
<dl class="field-list">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><dl>
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+30.g0da3a7d)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+33.gadd5fe9)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a
shapefile (str); or (2) a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code>.</p>
</dd>
<dt><strong>name</strong><span class="classifier"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a></span></dt><dd><p>Name to be assigned to the point dataset.</p>
Expand All @@ -1202,7 +1205,7 @@ <h1>spaghetti.Network<a class="headerlink" href="#spaghetti-network" title="Perm
</dd>
</dl>
<p class="rubric">Notes</p>
<p>See <a class="bibtex reference internal" href="../references.html#doi-10-1111-gean-12211" id="id27">[GFH19]</a> for a detailed discussion on
<p>See <a class="bibtex reference internal" href="../references.html#doi-10-1111-gean-12211" id="id28">[GFH19]</a> for a detailed discussion on
the modeling consequences of snapping points to spatial networks.</p>
<p class="rubric">Examples</p>
<p>Instantiate a network.</p>
Expand Down
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Expand Up @@ -139,8 +139,10 @@ <h1>spaghetti.PointPattern<a class="headerlink" href="#spaghetti-pointpattern" t
<dl class="field-list">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><dl>
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+30.g0da3a7d)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a shapefile
<code class="docutils literal notranslate"><span class="pre">str</span></code>; or (2) a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code>.</p>
<dt><strong>in_data</strong><span class="classifier">{<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">list</span></code></a>, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">tuple</span></code></a>, <a class="reference external" href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.17)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a>, <a class="reference external" href="https://pysal.org/libpysal/generated/libpysal.cg.Point.html#libpysal.cg.Point" title="(in libpysal v4.2.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">libpysal.cg.Point</span></code></a>, <a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+33.gadd5fe9)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a>}</span></dt><dd><p>The input geographic data. Either (1) a path to a shapefile
(str); (2) an iterable containing <code class="docutils literal notranslate"><span class="pre">libpysal.cg.Point</span></code>
objects; (3) a single <code class="docutils literal notranslate"><span class="pre">libpysal.cg.Point</span></code>; or
(4) a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code>.</p>
</dd>
<dt><strong>idvariable</strong><span class="classifier"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="docutils literal notranslate"><span class="pre">str</span></code></a></span></dt><dd><p>Field in the shapefile to use as an ID variable.</p>
</dd>
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Expand Up @@ -159,11 +159,11 @@ <h1>spaghetti.element_as_gdf<a class="headerlink" href="#spaghetti-element-as-gd
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><dl>
<dt><strong>points</strong><span class="classifier"><a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+30.g0da3a7d)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a></span></dt><dd><p>Network point elements (either vertices or <code class="docutils literal notranslate"><span class="pre">network.PointPattern</span></code>
<dt><strong>points</strong><span class="classifier"><a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+33.gadd5fe9)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a></span></dt><dd><p>Network point elements (either vertices or <code class="docutils literal notranslate"><span class="pre">network.PointPattern</span></code>
points) as a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code> of <code class="docutils literal notranslate"><span class="pre">shapely.geometry.Point</span></code>
objects with an <code class="docutils literal notranslate"><span class="pre">&quot;id&quot;</span></code> column and <code class="docutils literal notranslate"><span class="pre">&quot;geometry&quot;&quot;</span></code> column.</p>
</dd>
<dt><strong>lines</strong><span class="classifier"><a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+30.g0da3a7d)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a></span></dt><dd><p>Network arc elements as a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code> of
<dt><strong>lines</strong><span class="classifier"><a class="reference external" href="https://geopandas.readthedocs.io/en/latest/reference/geopandas.GeoDataFrame.html#geopandas.GeoDataFrame" title="(in GeoPandas v0.6.1+33.gadd5fe9)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code></a></span></dt><dd><p>Network arc elements as a <code class="docutils literal notranslate"><span class="pre">geopandas.GeoDataFrame</span></code> of
<code class="docutils literal notranslate"><span class="pre">shapely.geometry.LineString</span></code> objects with an <code class="docutils literal notranslate"><span class="pre">&quot;id&quot;</span></code>
column and <code class="docutils literal notranslate"><span class="pre">&quot;geometry&quot;</span></code> column.</p>
</dd>
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