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Merge pull request #154 from TeaspoonTDA/fix_medical_data
Update documentation to include TADA paper link.
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doc_source/modules/DAF/DataAssimilation.rst

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Data Assimilation
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=========================================================
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This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, "`Topological Approach for Data Assimilation <https://arxiv.org>`_." We plan to implement more data assimilation tools here in the future.
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This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, "`Topological Approach for Data Assimilation <https://arxiv.org/abs/2411.18627>`_." We plan to implement more data assimilation tools here in the future.
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.. warning::
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`TADA` requires `tensorflow <https://www.tensorflow.org>`_ for optimization features. Please install teaspoon using the command: `pip install "teaspoon[full]"` to install the necessary packages.
@@ -76,3 +76,6 @@ This page gives a summary of the functions available in the data assimilation li
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print(f"TADA Forecast Time: {tada_time}")
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print(f"LR Forecast Time: {lr_time}")
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.. note::
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Resulting forecast times may vary depending on the operating system.

doc_source/modules/DAF/Forecasting.rst

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Output of example
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.. figure:: ../../figures/LR_forecast_example.png
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.. note::
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Forecast may vary depending on the operating system.

docs/_modules/teaspoon/ML/load_datasets.html

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<h1>Source code for teaspoon.ML.load_datasets</h1><div class="highlight"><pre>
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<span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
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<span class="kn">import</span> <span class="nn">importlib_resources</span>
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<span class="kn">from</span> <span class="nn">teaspoon.ML</span> <span class="kn">import</span> <span class="n">datasets</span>
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<div class="viewcode-block" id="mpeg7">
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<a class="viewcode-back" href="../../../modules/ML/DS.html#teaspoon.ML.load_datasets.mpeg7">[docs]</a>
@@ -161,8 +161,8 @@ <h1>Source code for teaspoon.ML.load_datasets</h1><div class="highlight"><pre>
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<span class="sd"> Load the persistence diagrams from the MPEG7 dataset</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="s1">&#39;datasets&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;mpeg7.pickle&#39;</span><span class="p">)</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="n">datasets</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;mpeg7.pickle&#39;</span><span class="p">)</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_pickle</span><span class="p">(</span><span class="n">stream</span><span class="p">)</span>
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<span class="k">return</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div>
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@@ -175,7 +175,7 @@ <h1>Source code for teaspoon.ML.load_datasets</h1><div class="highlight"><pre>
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<span class="sd"> Load the persistence diagrams from the shrec14 dataset</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="s1">&#39;datasets&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;shrec14.pickle&#39;</span><span class="p">)</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="n">datasets</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;shrec14.pickle&#39;</span><span class="p">)</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_pickle</span><span class="p">(</span><span class="n">stream</span><span class="p">)</span>
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<span class="k">return</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div>
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@@ -199,7 +199,7 @@ <h1>Source code for teaspoon.ML.load_datasets</h1><div class="highlight"><pre>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="s1">&#39;datasets&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;mnist.pickle&#39;</span><span class="p">)</span>
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<span class="n">stream</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="n">datasets</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;mnist.pickle&#39;</span><span class="p">)</span>
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<span class="n">data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_pickle</span><span class="p">(</span><span class="n">stream</span><span class="p">)</span>
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<span class="k">return</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div>
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docs/_modules/teaspoon/MakeData/DynSysLib/medical_data.html

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@@ -174,23 +174,23 @@ <h1>Source code for teaspoon.MakeData.DynSysLib.medical_data</h1><div class="hig
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<span class="sd"> .. [1] Ralph G Andrzejak, Klaus Lehnertz, Florian Mormann, Christoph Rieke, Peter David, and Christian E Elger. Indications of nonlinear deterministic and nite-dimensional structures in time series of brain electrical activity: Dependence on recording region and brain state. Physical Review E, 64(6):061907, 2001.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="n">path</span> <span class="o">=</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">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">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">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">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
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<span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">(),</span> <span class="s1">&#39;teaspoon&#39;</span><span class="p">),</span> <span class="s1">&#39;teaspoon&#39;</span><span class="p">),</span> <span class="s1">&#39;MakeData&#39;</span><span class="p">),</span> <span class="s1">&#39;DynSysLib&#39;</span><span class="p">),</span> <span class="s1">&#39;Data&#39;</span><span class="p">)</span>
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<span class="kn">import</span> <span class="nn">importlib_resources</span>
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<span class="kn">from</span> <span class="nn">teaspoon.MakeData.DynSysLib.Data</span> <span class="kn">import</span> <span class="n">EEG</span>
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<span class="k">if</span> <span class="n">dynamic_state</span> <span class="o">==</span> <span class="s1">&#39;normal&#39;</span><span class="p">:</span> <span class="c1"># healthy</span>
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<span class="n">path</span> <span class="o">=</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">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">path</span><span class="p">,</span> <span class="s1">&#39;EEG&#39;</span><span class="p">),</span> <span class="s1">&#39;Z093.txt&#39;</span><span class="p">)</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">skiprows</span><span class="o">=</span><span class="mi">1</span><span class="p">)[</span>
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<span class="mi">0</span><span class="p">:</span><span class="n">SampleSize</span><span class="p">]]</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="n">EEG</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;Z093.txt&#39;</span><span class="p">)</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">ts</span><span class="p">,</span> <span class="n">skiprows</span><span class="o">=</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">:</span><span class="n">SampleSize</span><span class="p">]]</span>
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<span class="k">if</span> <span class="n">dynamic_state</span> <span class="o">==</span> <span class="s1">&#39;seizure&#39;</span><span class="p">:</span> <span class="c1"># seizure</span>
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<span class="n">path</span> <span class="o">=</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">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">path</span><span class="p">,</span> <span class="s1">&#39;EEG&#39;</span><span class="p">),</span> <span class="s1">&#39;S056.txt&#39;</span><span class="p">)</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">skiprows</span><span class="o">=</span><span class="mi">1</span><span class="p">)[</span>
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<span class="mi">0</span><span class="p">:</span><span class="n">SampleSize</span><span class="p">]]</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="n">EEG</span><span class="p">)</span><span class="o">.</span><span class="n">joinpath</span><span class="p">(</span><span class="s1">&#39;S056.txt&#39;</span><span class="p">)</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">ts</span><span class="p">,</span> <span class="n">skiprows</span><span class="o">=</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">:</span><span class="n">SampleSize</span><span class="p">]]</span>
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<span class="n">fs</span> <span class="o">=</span> <span class="mf">173.61</span>
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<span class="n">t</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span><span class="o">/</span><span class="n">fs</span>
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<span class="n">t</span> <span class="o">=</span> <span class="n">t</span><span class="p">[</span><span class="o">-</span><span class="n">SampleSize</span><span class="p">:]</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="p">[(</span><span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">])[</span><span class="o">-</span><span class="n">SampleSize</span><span class="p">:]]</span>
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<span class="n">ts</span> <span class="o">=</span> <span class="n">ts</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="o">-</span><span class="n">SampleSize</span><span class="p">:]</span>
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<span class="k">return</span> <span class="n">t</span><span class="p">,</span> <span class="n">ts</span></div>
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docs/_sources/modules/DAF/DataAssimilation.rst.txt

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Data Assimilation
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=========================================================
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This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, "`Topological Approach for Data Assimilation <https://arxiv.org>`_." We plan to implement more data assimilation tools here in the future.
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This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, "`Topological Approach for Data Assimilation <https://arxiv.org/abs/2411.18627>`_." We plan to implement more data assimilation tools here in the future.
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.. warning::
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`TADA` requires `tensorflow <https://www.tensorflow.org>`_ for optimization features. Please install teaspoon using the command: `pip install "teaspoon[full]"` to install the necessary packages.
@@ -76,3 +76,6 @@ This page gives a summary of the functions available in the data assimilation li
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print(f"TADA Forecast Time: {tada_time}")
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print(f"LR Forecast Time: {lr_time}")
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.. note::
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Resulting forecast times may vary depending on the operating system.

docs/_sources/modules/DAF/Forecasting.rst.txt

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.. figure:: ../../figures/LR_forecast_example.png
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.. note::
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Forecast may vary depending on the operating system.

docs/doctrees/environment.pickle

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docs/modules/DAF/DataAssimilation.html

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<section id="data-assimilation">
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<h1><span class="section-number">2.6.2. </span>Data Assimilation<a class="headerlink" href="#data-assimilation" title="Link to this heading"></a></h1>
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<p>This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, “<a class="reference external" href="https://arxiv.org">Topological Approach for Data Assimilation</a>.” We plan to implement more data assimilation tools here in the future.</p>
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<p>This page gives a summary of the functions available in the data assimilation library. Differentiation of persistence diagrams is exploited to optimize data driven model coefficients by minimizing topological differences between model the model forecast and measurements. More information on the details of the TADA algorithm can be found in, “<a class="reference external" href="https://arxiv.org/abs/2411.18627">Topological Approach for Data Assimilation</a>.” We plan to implement more data assimilation tools here in the future.</p>
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<div class="admonition warning">
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<p class="admonition-title">Warning</p>
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<p><cite>TADA</cite> requires <a class="reference external" href="https://www.tensorflow.org">tensorflow</a> for optimization features. Please install teaspoon using the command: <cite>pip install “teaspoon[full]”</cite> to install the necessary packages.</p>
@@ -268,6 +268,10 @@ <h1><span class="section-number">2.6.2. </span>Data Assimilation<a class="header
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;LR Forecast Time: </span><span class="si">{</span><span class="n">lr_time</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
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</pre></div>
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</div>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>Resulting forecast times may vary depending on the operating system.</p>
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</div>
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</section>
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docs/modules/DAF/Forecasting.html

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<figure class="align-default">
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<img alt="../../_images/LR_forecast_example.png" src="../../_images/LR_forecast_example.png" />
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</figure>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>Forecast may vary depending on the operating system.</p>
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</div>
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</section>
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docs/searchindex.js

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pyproject.toml

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[project]
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name = "teaspoon"
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version = "1.5.17"
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version = "1.5.19"
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authors = [
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{ name="Elizabeth Munch", email="[email protected]" },
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{ name="Firas Khasawneh", email="[email protected]" },

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