Skip to content

Commit

Permalink
deploy: 287af33
Browse files Browse the repository at this point in the history
  • Loading branch information
@joshuailevy
joshuailevy committed Jan 30, 2024
0 parents commit 9244d8e
Show file tree
Hide file tree
Showing 192 changed files with 34,952 additions and 0 deletions.
4 changes: 4 additions & 0 deletions .buildinfo
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: eebb40b78c0e3e9c12f41205d97eb375
tags: 645f666f9bcd5a90fca523b33c5a78b7
Binary file added .doctrees/Cases_by_location.doctree
Binary file not shown.
Binary file added .doctrees/Global_Prev.doctree
Binary file not shown.
Binary file added .doctrees/Lineage_mutations.doctree
Binary file not shown.
Binary file added .doctrees/Mut_By_Lin.doctree
Binary file not shown.
Binary file added .doctrees/Outbreak_data Functions.doctree
Binary file not shown.
Binary file added .doctrees/Prevalence_by_location.doctree
Binary file not shown.
Binary file added .doctrees/Seq_counts.doctree
Binary file not shown.
Binary file added .doctrees/auth_setup.doctree
Binary file not shown.
Binary file added .doctrees/collection_date.doctree
Binary file not shown.
Binary file added .doctrees/daily_lag.doctree
Binary file not shown.
Binary file added .doctrees/daily_prev_by_location.doctree
Binary file not shown.
Binary file added .doctrees/environment.pickle
Binary file not shown.
Binary file added .doctrees/index.doctree
Binary file not shown.
Binary file added .doctrees/mutation_details.doctree
Binary file not shown.
Empty file added .nojekyll
Empty file.
183 changes: 183 additions & 0 deletions Cases_by_location.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,183 @@
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>cases_by_location(location) &mdash; Python Outbreak.info API 0.1 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/fonts.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->

<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=2709fde1"></script>
<script src="_static/doctools.js?v=888ff710"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
</head>

<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >



<a href="index.html" class="icon icon-home">
Python Outbreak.info API
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul>
<li class="toctree-l1"><a class="reference internal" href="auth_setup.html">authenticate_new_user()</a></li>
<li class="toctree-l1"><a class="reference internal" href="all_lineage_prevalences.html">all_lineage_prevalences(location, startswith)</a></li>
<li class="toctree-l1"><a class="reference internal" href="global_prevalence.html">global_prevalence(pango_lin, mutations, cumulative)</a></li>
<li class="toctree-l1"><a class="reference internal" href="mutations_by_lineage.html">mutations_by_lineage(mutation, location, pango_lin)</a></li>
<li class="toctree-l1"><a class="reference internal" href="lineage_by_sub_admin.html">lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)</a></li>
<li class="toctree-l1"><a class="reference internal" href="collection_date.html">collection_date(pango_lin, mutations=None, location=None)</a></li>
<li class="toctree-l1"><a class="reference internal" href="submission_date.html">submission_date(pango_lin, mutations=None, location)</a></li>
<li class="toctree-l1"><a class="reference internal" href="mutation_details.html">mutation_details(mutations)</a></li>
<li class="toctree-l1"><a class="reference internal" href="daily_lag.html">daily_lag(location=None)</a></li>
<li class="toctree-l1"><a class="reference internal" href="wildcard_lineage.html">wildcard_lineage(name)</a></li>
<li class="toctree-l1"><a class="reference internal" href="wildcard_location.html">wildcard_location(name)</a></li>
<li class="toctree-l1"><a class="reference internal" href="wildcard_mutations.html">wildcard_mutations(name)</a></li>
<li class="toctree-l1"><a class="reference internal" href="location_details.html">location_details(location)</a></li>
<li class="toctree-l1"><a class="reference internal" href="Outbreak_data_Functions.html">get_outbreak_data()</a></li>
<li class="toctree-l1"><a class="reference internal" href="growth_rates.html">growth_rates(lineage, location)</a></li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="epidem_analysis.html">Epidemiological data analyses</a></li>
<li class="toctree-l1"><a class="reference internal" href="lineage_prevalence.html">Lineage Prevalence Analyses</a></li>
<li class="toctree-l1"><a class="reference internal" href="mutation_analysis.html">Mutation Data Analyses</a></li>
<li class="toctree-l1"><a class="reference internal" href="cryptic_vars.html">Dealing with Cryptic Variants</a></li>
</ul>

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

<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">Python Outbreak.info API</a>
</nav>

<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">cases_by_location(location)</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/Cases_by_location.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<section id="cases-by-location-location">
<h1>cases_by_location(location)<a class="headerlink" href="#cases-by-location-location" title="Link to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="outbreak_data.cases_by_location">
<span class="sig-prename descclassname"><span class="pre">outbreak_data.</span></span><span class="sig-name descname"><span class="pre">cases_by_location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">location</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">server</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'api.outbreak.info'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pull_smoothed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#outbreak_data.cases_by_location" title="Link to this definition"></a></dt>
<dd><p>Loads data from a location if input is a string, or from multiple locations
if location is a list of string locations. Since this API endpoint supports paging, collect_all is used to return all data.</p>
<dl class="simple">
<dt>Arguments:</dt><dd><dl class="field-list simple">
<dt class="field-odd">location<span class="colon">:</span></dt>
<dd class="field-odd"><p>A string or list of strings, separate multiple locations by “,”</p>
</dd>
<dt class="field-even">pull_smoothed<span class="colon">:</span></dt>
<dd class="field-even"><p>For every value &gt;= 0, returns 1000 obs. (paging)</p>
</dd>
<dt class="field-odd">return<span class="colon">:</span></dt>
<dd class="field-odd"><p>A pandas dataframe</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>

<p>Example usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#Get the number of SARS-CoV-2 cases in Colorado.</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">outbreak_data</span><span class="o">.</span><span class="n">cases_by_location</span><span class="p">(</span><span class="s1">&#39;USA_US-CO&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
</pre></div>
</div>
<div class="literal-block-wrapper docutils container" id="id1">
<div class="code-block-caption"><span class="caption-text">Output:</span><a class="headerlink" href="#id1" title="Link to this code"></a></div>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">_id</span> <span class="n">_score</span> <span class="n">admin1</span> <span class="n">confirmed_numIncrease</span> \
<span class="mi">0</span> <span class="n">USA_Colorado_None2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">14</span> <span class="mf">8.438688</span> <span class="n">Colorado</span> <span class="mi">505</span>
<span class="mi">1</span> <span class="n">USA_Colorado_None2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">18</span> <span class="mf">8.438688</span> <span class="n">Colorado</span> <span class="mi">1060</span>
<span class="mi">2</span> <span class="n">USA_Colorado_None2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">20</span> <span class="mf">8.438688</span> <span class="n">Colorado</span> <span class="mi">852</span>
<span class="mi">3</span> <span class="n">USA_Colorado_None2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">26</span> <span class="mf">8.438688</span> <span class="n">Colorado</span> <span class="mi">1184</span>
<span class="mi">4</span> <span class="n">USA_Colorado_None2021</span><span class="o">-</span><span class="mi">04</span><span class="o">-</span><span class="mi">07</span> <span class="mf">8.438688</span> <span class="n">Colorado</span> <span class="mi">1897</span>
<span class="o">...</span> <span class="o">...</span> <span class="o">...</span> <span class="o">...</span> <span class="o">...</span>
<span class="mi">1116</span> <span class="n">USA_Colorado_None2022</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">22</span> <span class="mf">8.397695</span> <span class="n">Colorado</span> <span class="mi">2226</span>
<span class="mi">1117</span> <span class="n">USA_Colorado_None2022</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">29</span> <span class="mf">8.397695</span> <span class="n">Colorado</span> <span class="mi">2402</span>
<span class="mi">1118</span> <span class="n">USA_Colorado_None2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">09</span> <span class="mf">8.397695</span> <span class="n">Colorado</span> <span class="mi">1348</span>
<span class="mi">1119</span> <span class="n">USA_Colorado_None2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">14</span> <span class="mf">8.397695</span> <span class="n">Colorado</span> <span class="mi">1924</span>
<span class="mi">1120</span> <span class="n">USA_Colorado_None2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">16</span> <span class="mf">8.397695</span> <span class="n">Colorado</span> <span class="mi">1231</span>

<span class="n">date</span>
<span class="mi">0</span> <span class="mi">2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">14</span>
<span class="mi">1</span> <span class="mi">2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">18</span>
<span class="mi">2</span> <span class="mi">2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">20</span>
<span class="mi">3</span> <span class="mi">2021</span><span class="o">-</span><span class="mi">03</span><span class="o">-</span><span class="mi">26</span>
<span class="mi">4</span> <span class="mi">2021</span><span class="o">-</span><span class="mi">04</span><span class="o">-</span><span class="mi">07</span>
<span class="o">...</span> <span class="o">...</span>
<span class="mi">1116</span> <span class="mi">2022</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">22</span>
<span class="mi">1117</span> <span class="mi">2022</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">29</span>
<span class="mi">1118</span> <span class="mi">2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">09</span>
<span class="mi">1119</span> <span class="mi">2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">14</span>
<span class="mi">1120</span> <span class="mi">2022</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">16</span>
</pre></div>
</div>
</div>
<p>[1121 rows x 5 columns]</p>
</section>


</div>
</div>
<footer>

<hr/>

<div role="contentinfo">
<p>&#169; Copyright .</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.


</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>

</body>
</html>
Loading

0 comments on commit 9244d8e

Please sign in to comment.