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Tutorials
=========


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Guide step by step
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Outline of the process and steps required to compute various metrics.



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    <div class="sphx-glr-thumbcontainer" tooltip="Step 01 - Compute AMR metrics">

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  .. image:: /_examples/tutorial/guide/images/thumb/sphx_glr_plot_step_01_thumb.png
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  :ref:`sphx_glr__examples_tutorial_guide_plot_step_01.py`

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      <div class="sphx-glr-thumbnail-title">Step 01 - Compute AMR metrics</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will explore how to compute a time series from susceptibility test data and...">

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  .. image:: /_examples/tutorial/guide/images/thumb/sphx_glr_plot_step_02_thumb.png
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  :ref:`sphx_glr__examples_tutorial_guide_plot_step_02.py`

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      <div class="sphx-glr-thumbnail-title">Step 02 - Temporal evolution</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial example, we will delve into the fascinating field of time series analysis and ...">

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  .. image:: /_examples/tutorial/guide/images/thumb/sphx_glr_plot_step_03_thumb.png
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  :ref:`sphx_glr__examples_tutorial_guide_plot_step_03.py`

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      <div class="sphx-glr-thumbnail-title">Step 03 - Time Series Analysis</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will learn about important concepts such as time series decomposition, auto...">

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  .. image:: /_examples/tutorial/guide/images/thumb/sphx_glr_plot_step_04_thumb.png
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  :ref:`sphx_glr__examples_tutorial_guide_plot_step_04.py`

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      <div class="sphx-glr-thumbnail-title">Step 04 - TSA to estimate trends</div>
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Computing AMR metrics
---------------------

Examples with the most important metrics.


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    <div class="sphx-glr-thumbcontainer" tooltip="The Single Antimicrobial Resistance Index or SARI describes the proportion of resistant isolate...">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_a_sari_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_a_sari.py`

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      <div class="sphx-glr-thumbnail-title">Single Antimicrobial Resistance (``SARI``)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The Antimicrobial Spectrum of Activity Index or ASAI refers to the range of microbe species tha...">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_b_asai_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_b_asai.py`

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      <div class="sphx-glr-thumbnail-title">Spectrum of Activity (``ASAI``)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Determination of the Multiple Antimicrobial Resistance Index or MARI follows the procedure desc...">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_c_mari_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_c_mari.py`

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      <div class="sphx-glr-thumbnail-title">Multiple Resistance (``MARI``)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Single Resistance Trend (``SART``)">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_d_sart_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_d_sart.py`

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      <div class="sphx-glr-thumbnail-title">Single Resistance Trend (``SART``)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The Drug Resistance Index or DRI measures changes through time in the proportion of disease-cau...">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_e_dri_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_e_dri.py`

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      <div class="sphx-glr-thumbnail-title">Drug Resistance Index (``DRI``)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The Collateral Sensitivity Index - ACSI ...">

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  .. image:: /_examples/tutorial/indexes/images/thumb/sphx_glr_plot_core_f_acri_thumb.png
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  :ref:`sphx_glr__examples_tutorial_indexes_plot_core_f_acri.py`

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      <div class="sphx-glr-thumbnail-title">Collateral Sensitivity Index (``ACSI``)</div>
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Metrics
-------

Examples computing metrics.


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    <div class="sphx-glr-thumbcontainer" tooltip="Example with the &#x27;errors&#x27; or scores implemented.">

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  .. image:: /_examples/tutorial/metrics/images/thumb/sphx_glr_plot_metrics_scores_thumb.png
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  :ref:`sphx_glr__examples_tutorial_metrics_plot_metrics_scores.py`

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      <div class="sphx-glr-thumbnail-title">Metrics - errors</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Example to show how to use the SigmoidA class to compute weights.">

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  .. image:: /_examples/tutorial/metrics/images/thumb/sphx_glr_plot_metrics_weights_thumb.png
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  :ref:`sphx_glr__examples_tutorial_metrics_plot_metrics_weights.py`

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      <div class="sphx-glr-thumbnail-title">Metrics - weights</div>
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Time-series analysis (regression)
---------------------------------

Examples using regression and time-series analysis.


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    <div class="sphx-glr-thumbcontainer" tooltip="In non-parametric statistics, the Theil–Sen estimator is a method for robustly fitting a line t...">

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  .. image:: /_examples/tutorial/regression/images/thumb/sphx_glr_plot_core_regression_a_theilsens_thumb.png
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  :ref:`sphx_glr__examples_tutorial_regression_plot_core_regression_a_theilsens.py`

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      <div class="sphx-glr-thumbnail-title">Using Theil-Sen estimator</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Approximating a function using Weighted Least Squares (WLS)">

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  .. image:: /_examples/tutorial/regression/images/thumb/sphx_glr_plot_core_regression_b_wls_thumb.png
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  :ref:`sphx_glr__examples_tutorial_regression_plot_core_regression_b_wls.py`

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      <div class="sphx-glr-thumbnail-title">Using weighted least squares (WLS)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Approximate a function using Autoregressive Integrated Moving Average (ARIMA)">

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  .. image:: /_examples/tutorial/regression/images/thumb/sphx_glr_plot_core_regression_c_arima_thumb.png
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  :ref:`sphx_glr__examples_tutorial_regression_plot_core_regression_c_arima.py`

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      <div class="sphx-glr-thumbnail-title">Using autoregressive model ARIMA</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Approximate a function using Sesonal Autoregressive Integrated Moving Average (SARIMA)">

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  .. image:: /_examples/tutorial/regression/images/thumb/sphx_glr_plot_core_regression_d_sarimax_thumb.png
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  :ref:`sphx_glr__examples_tutorial_regression_plot_core_regression_d_sarimax.py`

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      <div class="sphx-glr-thumbnail-title">Using SARIMAX for seasonality</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This method shows an ensemble method that combines the use of Weighted Linear Regression (WLS) ...">

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  .. image:: /_examples/tutorial/regression/images/thumb/sphx_glr_plot_core_regression_e_ensemble_thumb.png
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  :ref:`sphx_glr__examples_tutorial_regression_plot_core_regression_e_ensemble.py`

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      <div class="sphx-glr-thumbnail-title">Using an ensemble WLS + ARMA</div>
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Using the statistical tests wrappers
------------------------------------

Examples using some wrappers implemented to compute statistical tests.


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    <div class="sphx-glr-thumbcontainer" tooltip="The Augmented Dickey-Fuller test...">

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  .. image:: /_examples/tutorial/statistics/images/thumb/sphx_glr_plot_core_stats_adfuller_thumb.png
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  :ref:`sphx_glr__examples_tutorial_statistics_plot_core_stats_adfuller.py`

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      <div class="sphx-glr-thumbnail-title">ADFuller</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Example using your package">

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  .. image:: /_examples/tutorial/statistics/images/thumb/sphx_glr_plot_core_stats_correlation_thumb.png
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  :ref:`sphx_glr__examples_tutorial_statistics_plot_core_stats_correlation.py`

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      <div class="sphx-glr-thumbnail-title">Correlation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Example using your package">

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  .. image:: /_examples/tutorial/statistics/images/thumb/sphx_glr_plot_core_stats_kendall_thumb.png
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  :ref:`sphx_glr__examples_tutorial_statistics_plot_core_stats_kendall.py`

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      <div class="sphx-glr-thumbnail-title">Kendall</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Example using your package">

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  .. image:: /_examples/tutorial/statistics/images/thumb/sphx_glr_plot_core_stats_stationarity_thumb.png
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  :ref:`sphx_glr__examples_tutorial_statistics_plot_core_stats_stationarity.py`

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      <div class="sphx-glr-thumbnail-title">Stationarity</div>
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.. toctree::
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   :includehidden:


   /../source/_examples/tutorial/guide/index.rst
   /../source/_examples/tutorial/indexes/index.rst
   /../source/_examples/tutorial/metrics/index.rst
   /../source/_examples/tutorial/regression/index.rst
   /../source/_examples/tutorial/statistics/index.rst



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