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CDCgov · Jun 7, 2023 · 28a785b · 28a785b
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diff --git a/_modules/pynssp/core/container.html b/_modules/pynssp/core/container.html
@@ -99,24 +99,33 @@ <h1>Source code for pynssp.core.container</h1><div class="highlight"><pre>
 
 <span class="sd">    An object of class NSSPContainer stores a value or an object</span>
 <span class="sd">    The NSSPContainer class encapsulates a value or an object</span>
+
+<span class="sd">    :param value: value to store</span>
+<span class="sd">    :ivar value: Stored value</span>
+<span class="sd">    :examples:</span>
+
+<span class="sd">      &gt;&gt;&gt; from pynssp import NSSPContainer</span>
+<span class="sd">      &gt;&gt;&gt; </span>
+<span class="sd">      &gt;&gt;&gt; cont = NSSPContainer(&quot;abcdef&quot;)</span>
 <span class="sd">  &quot;&quot;&quot;</span>
 
   <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Initializes an NSSPContainer class</span>
-
-<span class="sd">    :param value: value to store</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">value</span></div>
 
 
 <div class="viewcode-block" id="APIGraph"><a class="viewcode-back" href="../../../pynssp.core.html#pynssp.core.container.APIGraph">[docs]</a><span class="k">class</span> <span class="nc">APIGraph</span><span class="p">:</span>
-<span class="w">  </span><span class="sd">&quot;&quot;&quot;A class to store an API graph&quot;&quot;&quot;</span>
-
-  <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">response</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Initializes an APIGraph class</span>
+<span class="w">  </span><span class="sd">&quot;&quot;&quot;A class to store an API graph</span>
 
 <span class="sd">    :param path: a string representing the location of a graph</span>
 <span class="sd">    :param response: an object of class response</span>
+<span class="sd">    :ivar path: the location of a graph file</span>
+<span class="sd">    :ivar response: a response object</span>
+<span class="sd">  &quot;&quot;&quot;</span>
+
+  <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">response</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Initializes an APIGraph class</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span>
     <span class="bp">self</span><span class="o">.</span><span class="n">response</span> <span class="o">=</span> <span class="n">response</span>

diff --git a/_modules/pynssp/core/credentials.html b/_modules/pynssp/core/credentials.html
@@ -109,14 +109,19 @@ <h1>Source code for pynssp.core.credentials</h1><div class="highlight"><pre>
 
 <span class="sd">    A Credentials object has a username, a password and a key.</span>
 <span class="sd">    A Credentials object gets API data via an API URL.</span>
+
+<span class="sd">    :param username: a string for username (Default username = None)</span>
+<span class="sd">    :param password: a string for password (Default password = None)</span>
+
+<span class="sd">    :examples:</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import Credentials</span>
+<span class="sd">        &gt;&gt;&gt; </span>
+<span class="sd">        &gt;&gt;&gt; myProfile = Credentials(&quot;user&quot;, &quot;pass&quot;)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">username</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">password</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Initializes a new Credentials object.</span>
-
-<span class="sd">        :param username: a string for username (Default username = None)</span>
-<span class="sd">        :param password: a string for password (Default password = None)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">__k</span> <span class="o">=</span> <span class="n">Fernet</span><span class="p">(</span><span class="n">Fernet</span><span class="o">.</span><span class="n">generate_key</span><span class="p">())</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">__username</span> <span class="o">=</span> <span class="n">NSSPContainer</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__k</span><span class="o">.</span><span class="n">encrypt</span><span class="p">(</span><span class="n">username</span><span class="o">.</span><span class="n">encode</span><span class="p">()))</span> \

diff --git a/_modules/pynssp/core/token.html b/_modules/pynssp/core/token.html
@@ -109,14 +109,21 @@ <h1>Source code for pynssp.core.token</h1><div class="highlight"><pre>
 
 <span class="sd">    A Token object has a token string and a key.</span>
 <span class="sd">    A Token object can get API data via an API URL.</span>
+
+<span class="sd">    :param token: a token string</span>
+<span class="sd">    :param access_token: type of HTTP authentication. </span>
+<span class="sd">        Should be &quot;Bearer&quot; or &quot;Basic&quot;. (Default value = &quot;Bearer&quot;)</span>
+<span class="sd">    :ivar access_token: HTTP authentication type.</span>
+
+<span class="sd">    :examples:</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import Token</span>
+<span class="sd">        &gt;&gt;&gt; </span>
+<span class="sd">        &gt;&gt;&gt; myTokenProfile = Token(&quot;abc123&quot;)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">token</span><span class="p">,</span> <span class="n">access_token</span><span class="o">=</span><span class="s2">&quot;Bearer&quot;</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Initializes a new Token object.</span>
-<span class="sd">        </span>
-<span class="sd">        :param token: a token string</span>
-<span class="sd">        :param access_token: type of HTTP authentication. Should be `Bearer` or `Basic`. (Default value = &quot;Bearer&quot;)</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">__k</span> <span class="o">=</span> <span class="n">Fernet</span><span class="p">(</span><span class="n">Fernet</span><span class="o">.</span><span class="n">generate_key</span><span class="p">())</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">__token</span> <span class="o">=</span> <span class="n">NSSPContainer</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__k</span><span class="o">.</span><span class="n">encrypt</span><span class="p">(</span><span class="n">token</span><span class="o">.</span><span class="n">encode</span><span class="p">()))</span>
@@ -128,7 +135,6 @@ <h1>Source code for pynssp.core.token</h1><div class="highlight"><pre>
 
 <span class="sd">        :param url: a string of API URL</span>
 <span class="sd">        :returns: an object of class response</span>
-
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">headers</span> <span class="o">=</span> <span class="p">{</span>
             <span class="s2">&quot;Authorization&quot;</span><span class="p">:</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span>
@@ -175,7 +181,6 @@ <h1>Source code for pynssp.core.token</h1><div class="highlight"><pre>
 
 <span class="sd">        :param file_ext: a non-empty character vector giving the file extension. (Default value = &quot;.pkl&quot;)</span>
 <span class="sd">        :param file:  (Default value = None)</span>
-
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="kn">from</span> <span class="nn">pickle</span> <span class="kn">import</span> <span class="n">dump</span>
         <span class="n">file_name</span> <span class="o">=</span> <span class="s2">&quot;tokenProfile&quot;</span> <span class="o">+</span> <span class="n">file_ext</span>

diff --git a/_modules/pynssp/data.html b/_modules/pynssp/data.html
@@ -103,18 +103,19 @@ <h1>Source code for pynssp.data</h1><div class="highlight"><pre>
 
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.data import *</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp.data import load_simulated_ts</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; simulated_ts = load_simulated_ts()</span>
 <span class="sd">        &gt;&gt;&gt; simulated_ts.info()</span>
-<span class="sd">        ... ## #   Column  Non-Null Count  Dtype</span>
-<span class="sd">        ... ## ---  ------  --------------  -----</span>
-<span class="sd">        ... ## 0   date    626 non-null    object</span>
-<span class="sd">        ... ## 1   week    626 non-null    int64</span>
-<span class="sd">        ... ## 2   year    626 non-null    int64</span>
-<span class="sd">        ... ## 3   cases   626 non-null    int64</span>
-<span class="sd">        ... ## 4   id      626 non-null    object</span>
-<span class="sd">        ... ## dtypes: int64(3), object(2)</span>
-<span class="sd">        ... ## memory usage: 24.6+ KB</span>
+<span class="sd">        ## #   Column  Non-Null Count  Dtype</span>
+<span class="sd">        ## ---  ------  --------------  -----</span>
+<span class="sd">        ## 0   date    626 non-null    object</span>
+<span class="sd">        ## 1   week    626 non-null    int64</span>
+<span class="sd">        ## 2   year    626 non-null    int64</span>
+<span class="sd">        ## 3   cases   626 non-null    int64</span>
+<span class="sd">        ## 4   id      626 non-null    object</span>
+<span class="sd">        ## dtypes: int64(3), object(2)</span>
+<span class="sd">        ## memory usage: 24.6+ KB</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">stream</span> <span class="o">=</span> <span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="s2">&quot;data/simulated_ts.csv&quot;</span><span class="p">)</span>
@@ -123,9 +124,11 @@ <h1>Source code for pynssp.data</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="get_scenario1"><a class="viewcode-back" href="../../pynssp.html#pynssp.data.get_scenario1">[docs]</a><span class="k">def</span> <span class="nf">get_scenario1</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a subset of the simulated time series data (&#39;scenario #1&#39;).</span>
+
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.data import *</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import get_scenario1</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; scenario1_ts = get_scenario1()</span>
 <span class="sd">        &gt;&gt;&gt; scenario1_ts.info()</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -135,9 +138,11 @@ <h1>Source code for pynssp.data</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="get_scenario2"><a class="viewcode-back" href="../../pynssp.html#pynssp.data.get_scenario2">[docs]</a><span class="k">def</span> <span class="nf">get_scenario2</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a subset of the simulated time series data (&#39;scenario #2&#39;).</span>
+
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.data import *</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import get_scenario2</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; scenario2_ts = get_scenario2()</span>
 <span class="sd">        &gt;&gt;&gt; scenario2_ts.info()</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -150,15 +155,16 @@ <h1>Source code for pynssp.data</h1><div class="highlight"><pre>
 
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.data import *</span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import load_nssp_stopwords</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; stopwords = load_nssp_stopwords()</span>
 <span class="sd">        &gt;&gt;&gt; stopwords.info()</span>
-<span class="sd">        ... ## #   Column      Non-Null Count  Dtype</span>
-<span class="sd">        ... ## ---  ------      --------------  -----</span>
-<span class="sd">        ... ## 1   word        835 non-null    object</span>
-<span class="sd">        ... ## 2   type        835 non-null    object</span>
-<span class="sd">        ... ## dtypes: int64(1), object(2)</span>
-<span class="sd">        ... ## memory usage: 13.2+ KB</span>
+<span class="sd">        ## #   Column      Non-Null Count  Dtype</span>
+<span class="sd">        ## ---  ------      --------------  -----</span>
+<span class="sd">        ## 1   word        835 non-null    object</span>
+<span class="sd">        ## 2   type        835 non-null    object</span>
+<span class="sd">        ## dtypes: int64(1), object(2)</span>
+<span class="sd">        ## memory usage: 13.2+ KB</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">stream</span> <span class="o">=</span> <span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="s2">&quot;data/nssp_stopwords.csv&quot;</span><span class="p">)</span>

diff --git a/_modules/pynssp/detectors/ewma.html b/_modules/pynssp/detectors/ewma.html
@@ -269,13 +269,15 @@ <h1>Source code for pynssp.detectors.ewma</h1><div class="highlight"><pre>
 <span class="sd">    :returns: Original pandas data frame with detection results.</span>
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import alert_ewma</span>
 <span class="sd">        &gt;&gt;&gt; import pandas as pd</span>
 <span class="sd">        &gt;&gt;&gt; import numpy as np</span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.detectors.ewma import *</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df = pd.DataFrame({</span>
 <span class="sd">        ...     &quot;date&quot;: pd.date_range(&quot;2020-01-01&quot;, &quot;2020-12-31&quot;),</span>
 <span class="sd">        ...     &quot;count&quot;: np.random.randint(0, 101, size=366)</span>
 <span class="sd">        ... })</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df_ewma = alert_ewma(df)</span>
 <span class="sd">        &gt;&gt;&gt; df_ewma.head()</span>
 <span class="sd">    &quot;&quot;&quot;</span>

diff --git a/_modules/pynssp/detectors/nbinom.html b/_modules/pynssp/detectors/nbinom.html
@@ -224,12 +224,15 @@ <h1>Source code for pynssp.detectors.nbinom</h1><div class="highlight"><pre>
 <span class="sd">        whether or not a time term was included.</span>
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
+<span class="sd">        &gt;&gt;&gt; from pnssp import alert_nbinom</span>
 <span class="sd">        &gt;&gt;&gt; import pandas as pd</span>
 <span class="sd">        &gt;&gt;&gt; import numpy as np</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df = pd.DataFrame({</span>
 <span class="sd">        ...    &quot;date&quot;: pd.date_range(start=&quot;2014-01-05&quot;, end=&quot;2022-02-05&quot;, freq=&quot;W&quot;),</span>
 <span class="sd">        ...    &quot;count&quot;: np.random.poisson(lam=25, size=(len(pd.date_range(start=&quot;2014-01-05&quot;, end=&quot;2022-02-05&quot;, freq=&quot;W&quot;)),))</span>
 <span class="sd">        ... })</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df_nbinom = alert_nbinom(df, baseline_end = &quot;2020-03-01&quot;)</span>
 <span class="sd">        &gt;&gt;&gt; df_nbinom.head()</span>
 <span class="sd">    &quot;&quot;&quot;</span>

diff --git a/_modules/pynssp/detectors/regression.html b/_modules/pynssp/detectors/regression.html
@@ -259,13 +259,15 @@ <h1>Source code for pynssp.detectors.regression</h1><div class="highlight"><pre>
 <span class="sd">    :returns: Original pandas data frame with detection results.</span>
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import alert_regression</span>
 <span class="sd">        &gt;&gt;&gt; import pandas as pd</span>
 <span class="sd">        &gt;&gt;&gt; import numpy as np</span>
-<span class="sd">        &gt;&gt;&gt; from pynssp.detectors.regression import *</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df = pd.DataFrame({</span>
 <span class="sd">        ...    &quot;date&quot;: pd.date_range(&quot;2020-01-01&quot;, &quot;2020-12-31&quot;),</span>
 <span class="sd">        ...    &quot;count&quot;: np.random.randint(0, 101, size=366)</span>
 <span class="sd">        ... })</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df_regression = alert_regression(df)</span>
 <span class="sd">        &gt;&gt;&gt; df_regression.head()</span>
 

diff --git a/_modules/pynssp/detectors/serfling.html b/_modules/pynssp/detectors/serfling.html
@@ -176,12 +176,15 @@ <h1>Source code for pynssp.detectors.serfling</h1><div class="highlight"><pre>
 <span class="sd">        a binary alarm indicator field, and a binary indicator</span>
 <span class="sd">    :examples:</span>
 <span class="sd">    </span>
+<span class="sd">        &gt;&gt;&gt; from pynssp import alert_serfling</span>
 <span class="sd">        &gt;&gt;&gt; import pandas as pd</span>
 <span class="sd">        &gt;&gt;&gt; import numpy as np</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df = pd.DataFrame({</span>
 <span class="sd">        ...    &quot;date&quot;: pd.date_range(start=&quot;2014-01-05&quot;, end=&quot;2022-02-05&quot;, freq=&quot;W&quot;),</span>
 <span class="sd">        ...    &quot;count&quot;: np.random.poisson(lam=25, size=(len(pd.date_range(start=&quot;2014-01-05&quot;, end=&quot;2022-02-05&quot;, freq=&quot;W&quot;)),))</span>
 <span class="sd">        ... })</span>
+<span class="sd">        &gt;&gt;&gt; </span>
 <span class="sd">        &gt;&gt;&gt; df_serfling  = alert_serfling(df, baseline_end = &quot;2020-03-01&quot;)</span>
 <span class="sd">        &gt;&gt;&gt; df_serfling.head()</span>
 <span class="sd">    &quot;&quot;&quot;</span>