.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "content/user_guide/auto_examples/1single/plot_eof-smode.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_content_user_guide_auto_examples_1single_plot_eof-smode.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_content_user_guide_auto_examples_1single_plot_eof-smode.py:


Sparse PCA
========================

This example demonstrates the application of sparse PCA [1]_ to sea surface temperature data. Sparse PCA is an alternative to rotated PCA, where the components are sparse, often providing a more interpretable solution.

We replicate the analysis from the original paper [1]_, which identifies the ENSO (El Niño-Southern Oscillation) as the fourth mode, representing about 1% of the total variance. The original study focused on weekly sea surface temperatures from satellite data, whereas we use monthly data from ERSSTv5. Consequently, our results may not match exactly, but they should be quite similar.

References
----------
.. [1] Erichson, N. B. et al. Sparse Principal Component Analysis via Variable Projection. SIAM J. Appl. Math. 80, 977-1002 (2020).

.. GENERATED FROM PYTHON SOURCE LINES 14-23

.. code-block:: default


    # Load packages and data:
    import matplotlib.pyplot as plt
    import xarray as xr
    from cartopy.crs import EqualEarth, PlateCarree
    from matplotlib.gridspec import GridSpec

    import xeofs as xe








.. GENERATED FROM PYTHON SOURCE LINES 24-25

We use sea surface temperature data from 1990 to 2017, consistent with the original paper.

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.. code-block:: default


    sst = xr.tutorial.open_dataset("ersstv5")["sst"]
    sst = sst.sel(time=slice("1990", "2017"))








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We perform sparse PCA using the `alpha` and `beta` parameters, which define the sparsity imposed by the elastic net (refer to Table 1 in the paper). In our analysis, we set `alpha` to 1e-5, as specified by the authors. Although the authors do not specify a value for `beta`, it appears that the results are not highly sensitive to this parameter. Therefore, we use the default `beta` value of 1e-4.

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.. code-block:: default


    model = xe.single.SparsePCA(n_modes=4, alpha=1e-5)
    model.fit(sst, dim="time")
    expvar = model.explained_variance()
    expvar_ratio = model.explained_variance_ratio()
    components = model.components()
    scores = model.scores()








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The explained variance fraction confirms that the fourth mode explains about 1% of the total variance, which is consistent with the original paper.

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.. code-block:: default


    print("Explained variance: ", expvar.round(0).values)
    print("Relative: ", (expvar_ratio * 100).round(1).values)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Explained variance:  [34060.  1252.   963.   402.]
    Relative:  [86.   3.2  2.4  1. ]




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Examining the first four modes, we clearly identify ENSO as the fourth mode.

.. GENERATED FROM PYTHON SOURCE LINES 47-66

.. code-block:: default


    proj = EqualEarth(central_longitude=180)
    kwargs = {"cmap": "RdBu", "vmin": -0.05, "vmax": 0.05, "transform": PlateCarree()}

    fig = plt.figure(figsize=(10, 12))
    gs = GridSpec(4, 2, width_ratios=[1, 2])
    ax0 = [fig.add_subplot(gs[i, 0]) for i in range(4)]
    ax1 = [fig.add_subplot(gs[i, 1], projection=proj) for i in range(4)]

    for i, (a0, a1) in enumerate(zip(ax0, ax1)):
        scores.sel(mode=i + 1).plot(ax=a0)
        a1.coastlines(color=".5")
        components.sel(mode=i + 1).plot(ax=a1, **kwargs)

        a0.set_xlabel("")

    plt.tight_layout()
    plt.savefig("sparse_pca.jpg")




.. image-sg:: /content/user_guide/auto_examples/1single/images/sphx_glr_plot_eof-smode_001.png
   :alt: mode = 1, mode = 2, mode = 3, mode = 4, mode = 1, mode = 2, mode = 3, mode = 4
   :srcset: /content/user_guide/auto_examples/1single/images/sphx_glr_plot_eof-smode_001.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 7.744 seconds)


.. _sphx_glr_download_content_user_guide_auto_examples_1single_plot_eof-smode.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example




    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_eof-smode.py <plot_eof-smode.py>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_eof-smode.ipynb <plot_eof-smode.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_