Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
@actions-user
actions-user committed Feb 29, 2024
1 parent ba97c30 commit 99888da
Show file tree
Hide file tree
Showing 252 changed files with 46,441 additions and 1,143 deletions.
Binary file added _downloads/203b418e4a4d604663eea6a5c1037633/geosnap-visualize-indexplot_seq-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added ...ds/7951bf35557cb233145e9a0d7465fda3/geosnap-visualize-indexplot_seq-1.hires.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _downloads/968d4ead8e5e1095d224e3e33676c074/geosnap-visualize-indexplot_seq-1.pdf
View file
Binary file not shown.
6 changes: 6 additions & 0 deletions _downloads/c838af3ae5fbb69ae7cccae2c0c8b488/geosnap-visualize-indexplot_seq-1.py
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
import pandas as pd
from geosnap.visualize import indexplot_seq
import matplotlib.pyplot as plt
df_LA = pd.read_csv("../../examples/data/LA_sequences.csv", converters={'GEO2010': lambda x: str(x)})
indexplot_seq(df_LA, clustering="seqC1", palette="pastel", ncols=3)
plt.show()
Binary file added _images/geosnap-visualize-indexplot_seq-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/geosnap_long.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
841 changes: 841 additions & 0 deletions _modules/geosnap/_data.html
View file

Large diffs are not rendered by default.

956 changes: 956 additions & 0 deletions _modules/geosnap/analyze/_model_results.html
View file

Large diffs are not rendered by default.

773 changes: 773 additions & 0 deletions _modules/geosnap/analyze/dynamics.html
View file

Large diffs are not rendered by default.

825 changes: 825 additions & 0 deletions _modules/geosnap/analyze/geodemo.html
View file

Large diffs are not rendered by default.

310 changes: 310 additions & 0 deletions _modules/geosnap/analyze/incs.html
View file

Large diffs are not rendered by default.

326 changes: 326 additions & 0 deletions _modules/geosnap/analyze/network.html
View file

Large diffs are not rendered by default.

346 changes: 346 additions & 0 deletions _modules/geosnap/analyze/segdyn.html
View file

Large diffs are not rendered by default.

378 changes: 378 additions & 0 deletions _modules/geosnap/harmonize/harmonize.html
View file

Large diffs are not rendered by default.

809 changes: 809 additions & 0 deletions _modules/geosnap/io/constructors.html
View file

Large diffs are not rendered by default.

205 changes: 205 additions & 0 deletions _modules/geosnap/io/gadm.html
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,205 @@
<!DOCTYPE html>

<html lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>geosnap.io.gadm &#8212; geosnap v0.13.1 Manual</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
<link rel="stylesheet" type="text/css" href="../../../_static/bootstrap-sphinx.css?v=9afac83c" />
<link rel="stylesheet" type="text/css" href="../../../_static/plot_directive.css" />
<script src="../../../_static/documentation_options.js?v=b4617fb1"></script>
<script src="../../../_static/doctools.js?v=888ff710"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<link rel="icon" href="../../../_static/geosnap.ico"/>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />
<meta charset='utf-8'>
<meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
<meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
<meta name="apple-mobile-web-app-capable" content="yes">
<script type="text/javascript" src="../../../_static/js/jquery-1.12.4.min.js"></script>
<script type="text/javascript" src="../../../_static/js/jquery-fix.js"></script>
<script type="text/javascript" src="../../../_static/bootstrap-3.4.1/js/bootstrap.min.js"></script>
<script type="text/javascript" src="../../../_static/bootstrap-sphinx.js"></script>

</head><body>

<div id="navbar" class="navbar navbar-default navbar-fixed-top">
<div class="container">
<div class="navbar-header">
<!-- .btn-navbar is used as the toggle for collapsed navbar content -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="../../../index.html">
geosnap</a>
<span class="navbar-text navbar-version pull-left"><b>0.13.1</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
<ul class="nav navbar-nav">

<li><a href="../../../installation.html">Installation</a></li>
<li><a href="../../../api.html">API</a></li>
<li><a href="../../../data.html">Data</a></li>
<li><a href="https://oturns.github.io/geosnap-guide/">User Guide</a></li>
<li><a href="../../../references.html">References</a></li>


<li class="dropdown globaltoc-container">
<a role="button"
id="dLabelGlobalToc"
data-toggle="dropdown"
data-target="#"
href="../../../index.html">Site <b class="caret"></b></a>
<ul class="dropdown-menu globaltoc"
role="menu"
aria-labelledby="dLabelGlobalToc"><p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../installation.html#installing-a-released-version">Installing a released version</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../installation.html#installing-development-version">Installing development version</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../api.html">API</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../api.html#io-module">IO Module</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../api.html#analyze-module">Analyze Module</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../api.html#harmonize-module">Harmonize Module</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../api.html#visualize-module">Visualize Module</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../api.html#util-module">Util Module</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../../../references.html">References</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../data.html">Data</a><ul>
<li class="toctree-l2"><a class="reference internal" href="../../../data.html#tabular-data">Tabular Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="../../../data.html#geo-data">Geo Data</a></li>
</ul>
</li>
</ul>
</ul>
</li>

<li class="dropdown">
<a role="button"
id="dLabelLocalToc"
data-toggle="dropdown"
data-target="#"
href="#">Page <b class="caret"></b></a>
<ul class="dropdown-menu localtoc"
role="menu"
aria-labelledby="dLabelLocalToc"></ul>
</li>






</ul>



<form class="navbar-form navbar-right" action="../../../search.html" method="get">
<div class="form-group">
<input type="text" name="q" class="form-control" placeholder="Search" />
</div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>

</div>
</div>
</div>

<div class="container">
<div class="row">
<div class="body col-md-12 content" role="main">

<h1>Source code for geosnap.io.gadm</h1><div class="highlight"><pre>
<span></span><span class="sd">&quot;&quot;&quot;Utilities for fetching data from GADM.&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">tempfile</span>

<span class="kn">import</span> <span class="nn">geopandas</span> <span class="k">as</span> <span class="nn">gpd</span>


<div class="viewcode-block" id="get_gadm">
<a class="viewcode-back" href="../../../generated/geosnap.io.get_gadm.html#geosnap.io.get_gadm">[docs]</a>
<span class="k">def</span> <span class="nf">get_gadm</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">use_fsspec</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">gpkg</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">n_retries</span><span class="o">=</span><span class="mi">3</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Collect data from GADM as a geodataframe.</span>

<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> code : str</span>
<span class="sd"> three character ISO code for a country</span>
<span class="sd"> level : int, optional</span>
<span class="sd"> which geometry level to collect, by default 0</span>
<span class="sd"> use_fsspec : bool</span>
<span class="sd"> whether to use the `fsspec` library</span>
<span class="sd"> gpkg : bool</span>
<span class="sd"> whether to read from a geopackage or shapefile. If True,</span>
<span class="sd"> geopackage will be read; shapefile if False. Ignored if using fsspec</span>
<span class="sd"> n_retries : int optional</span>
<span class="sd"> number of retries in case read fails from direct stream from GADM.</span>
<span class="sd"> Ignored if using fsspec.</span>

<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> geopandas.GeoDataFrame</span>
<span class="sd"> geodataframe containing GADM data</span>

<span class="sd"> Notes</span>
<span class="sd"> -------</span>
<span class="sd"> If not using the fsspec package, this function uses fiona&#39;s syntax to read a geodataframe directly with</span>
<span class="sd"> geopandas `read_file` function. Unfortunately, sometimes the operation fails</span>
<span class="sd"> before the read is complete resulting in an error--or occasionally, a</span>
<span class="sd"> geodataframe with missing rows. Repeating the call sometimes helps.</span>

<span class="sd"> When using fsspec, the function doesn&#39;t suffer these issues, but requires an additional dependency.</span>
<span class="sd"> If fsspec is available, this function its syntax to store a temporary file which is then</span>
<span class="sd"> read in by geopandas. In theory, the file could be read into fsspec directly</span>
<span class="sd"> without storing it in a temporary directory, but when reading a bytestream of GPKG,</span>
<span class="sd"> geopandas does not allow the specification of a particular layer (so reading GPKG</span>
<span class="sd"> with this method would always returns the layer with index 0 in the geopackage file).</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">code</span> <span class="o">=</span> <span class="n">code</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
<span class="kn">import</span> <span class="nn">fsspec</span>

<span class="k">with</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">TemporaryDirectory</span><span class="p">()</span> <span class="k">as</span> <span class="n">temp_path</span><span class="p">:</span>
<span class="k">with</span> <span class="n">fsspec</span><span class="o">.</span><span class="n">open</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;simplecache::zip://*.gpkg::https://biogeo.ucdavis.edu/data/gadm3.6/gpkg/gadm36_</span><span class="si">{</span><span class="n">code</span><span class="si">}</span><span class="s2">_gpkg.zip&quot;</span><span class="p">,</span>
<span class="n">simplecache</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;cache_storage&quot;</span><span class="p">:</span> <span class="n">temp_path</span><span class="p">},</span>
<span class="p">):</span>
<span class="n">gdf</span> <span class="o">=</span> <span class="n">gpd</span><span class="o">.</span><span class="n">read_file</span><span class="p">(</span>
<span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_path</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">temp_path</span><span class="p">)[</span><span class="mi">0</span><span class="p">]),</span>
<span class="n">layer</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;gadm36_</span><span class="si">{</span><span class="n">code</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">level</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">return</span> <span class="n">gdf</span></div>

</pre></div>

</div>

</div>
</div>
<footer class="footer">
<div class="container">
<p class="pull-right">
<a href="#">Back to top</a>

<br/>


</p>
<p>
&copy; Copyright 2023, geosnap developers.<br/>
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 7.2.6.<br/>
</p>
</div>
</footer>
</body>
</html>
Loading

0 comments on commit 99888da

Please sign in to comment.