Merge pull request #23 from nicrie/develop

Develop

README.rst

@@ -1,23 +1,41 @@
-|badge1| |badge2| |badge3| |badge4| |badge5| |badge6|
+.. image:: examples/1eof/rotated_eof.jpg
+ :align: center
+ :width: 800
+ :alt: Comparison of standard, Varimax-rotated and Proxmax-rotated EOF analysis for temperature field over North America.
+Example_ showing North American surface temperature decomposed via EOF analysis, Varimax rotation and Promax rotation.
 
-.. |badge1| image:: https://img.shields.io/github/v/tag/nicrie/xeofs?label=Release
- :alt: GitHub tag (latest SemVer)
-.. |badge2| image:: https://img.shields.io/github/workflow/status/nicrie/xeofs/CI
+.. _Example: https://xeofs.readthedocs.io/en/stable/auto_examples/1eof/plot_rotated_eof.html#sphx-glr-auto-examples-1eof-plot-rotated-eof-py
+
+==================================================
+xeofs: Multi-dimensional EOF analysis and variants
+==================================================
+
+|badge_build_status| |badge_docs_status| |badge_version_pypi| |badge_conda_version| |badge_downloads| |badge_coverage| |badge_license| |badge_zenodo|
+
+.. |badge_version_pypi| image:: https://img.shields.io/pypi/v/xeofs
+ :alt: PyPI
+.. |badge_build_status| image:: https://img.shields.io/github/workflow/status/nicrie/xeofs/CI
  :alt: GitHub Workflow Status (event)
-.. |badge3| image:: https://readthedocs.org/projects/xeofs/badge/?version=latest
+.. |badge_docs_status| image:: https://readthedocs.org/projects/xeofs/badge/?version=latest
  :target: https://xeofs.readthedocs.io/en/latest/?badge=latest
  :alt: Documentation Status
-.. |badge4| image:: https://img.shields.io/pypi/dm/xeofs
+.. |badge_downloads_pypi| image:: https://img.shields.io/pypi/dm/xeofs
  :alt: PyPI - Downloads
-.. |badge5| image:: https://codecov.io/gh/nicrie/xeofs/branch/main/graph/badge.svg?token=8040ZDH6U7
+.. |badge_coverage| image:: https://codecov.io/gh/nicrie/xeofs/branch/main/graph/badge.svg?token=8040ZDH6U7
  :target: https://codecov.io/gh/nicrie/xeofs
-.. |badge6| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6323012.svg
+.. |badge_zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6323012.svg
  :target: https://doi.org/10.5281/zenodo.6323012
  :alt: DOI - Zenodo
+.. |badge_license| image:: https://img.shields.io/pypi/l/xeofs
+ :alt: License
+.. |badge_conda_version| image:: https://img.shields.io/conda/vn/conda-forge/xeofs
+ :alt: Conda (channel only)
+.. |badge_downloads_conda| image:: https://img.shields.io/conda/dn/conda-forge/xeofs
+ :alt: Conda downloads
+.. |badge_downloads| image:: https://static.pepy.tech/personalized-badge/xeofs?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads
+ :target: https://pepy.tech/project/xeofs
+ :alt: Total downloads
 
-=================================
-xeofs: EOF analysis and variants
-=================================
 Empirical orthogonal function (EOF) analysis, more commonly known as
 principal component analysis (PCA), is one of the most popular methods
 for dimension reduction and structure identification in Earth system sciences.
@@ -32,35 +50,36 @@ scientific community. Each of these implementations has its own strengths,
 which need to be highlighted (please `let me know`_, if I forgot any):
 
 
-EOF models
------------
+Available Models
+----------------
 
 ===================== ========== ========== ========== ========== ========== ==========
-Package eofs_ pyEOF_ xeof_ xMCA_ xmca2_ **xeofs**
+Package **xeofs** eofs_ pyEOF_ xeof_ xMCA_ xmca2_
 ===================== ========== ========== ========== ========== ========== ==========
-EOF analysis ✅ ✅ ✅ ✅ ✅ ✅
-Rotated EOF analysis ❌ ✅ ❌ ❌ ✅ ✅
-Complex EOF analysis ❌ ❌ ❌ ❌ ✅ ❌
-Multivariate EOF ✅ ❌ ❌ ❌ ❌ ✅
-MCA ❌ ❌ ❌ ✅ ✅ ❌
-Rotated MCA ❌ ❌ ❌ ❌ ✅ ❌
-Complex MCA ❌ ❌ ❌ ❌ ✅ ❌
-Multivariate MCA ❌ ❌ ❌ ❌ ❌ ❌
+EOF analysis ✅ ✅ ✅ ✅ ✅  ✅
+Rotated EOF analysis ✅ ❌ ✅ ❌ ❌  ✅
+Complex EOF analysis ❌ ❌ ❌ ❌ ❌  ✅
+Multivariate EOF ✅ ✅ ❌ ❌ ❌  ❌
+MCA ✅ ❌ ❌ ❌ ✅  ✅
+Rotated MCA ❌ ❌ ❌ ❌ ❌  ✅
+Complex MCA ❌ ❌ ❌ ❌ ❌  ✅
+Multivariate MCA ✅ ❌ ❌ ❌ ❌  ❌
 ===================== ========== ========== ========== ========== ========== ==========
 
 
 Additional features
 ----------------------
 
 ===================== ========== ========== ========== ========== ========== ==========
-Package eofs_ pyEOF_ xeof_ xMCA_ xmca2_ **xeofs**
+Package **xeofs** eofs_ pyEOF_ xeof_ xMCA_ xmca2_
 ===================== ========== ========== ========== ========== ========== ==========
-``numpy`` interface ✅ ❌ ❌ ❌ ✅ ✅
-``pandas`` interface ❌ ❌ ❌ ❌ ❌ ✅
-``xarray`` interface ? ✅ ✅ ✅ ✅ ✅
-Fast algorithm ❌ ✅ ❌ ❌ ❌ ✅
-Dask support ✅ ❌ ✅ ❌ ❌ ❌
-Arbitrary dimensions ❌ ❌ ❌ ❌ ❌ ✅
+``numpy`` interface ✅ ✅ ❌ ❌ ❌ ✅
+``pandas`` interface ✅ ❌ ❌ ❌ ❌ ❌
+``xarray`` interface ✅ ? ✅ ✅ ✅ ✅
+Fast algorithm ✅ ❌ ✅ ❌ ❌ ❌
+Dask support ❌ ✅ ❌ ✅ ❌ ❌
+Multi-dimensional ✅ ❌ ❌ ❌ ❌ ❌
+Significance analysis ✅ ❌ ❌ ❌ ❌ ❌
 ===================== ========== ========== ========== ========== ========== ==========
 
 
@@ -77,7 +96,7 @@ Why ``xeofs``?
 ----------------------
 
 The goal of ``xeofs`` is to merge these different implementations and to simplify the integration of other existing and future variants of EOF analysis thanks to its modular code structure.
-The official name is deliberately chosen to be similar to the other implementations to make it clear that ``xeofs`` is initially nothing revolutionary new in itself. The point is not to distinguish this implementation from the others, but rather to unify (+ extend) already existing implementations.
+The official name is deliberately chosen to be similar to the other implementations to make it clear that ``xeofs`` is nothing revolutionary new in itself. The point is not to distinguish this implementation from the others, but rather to unify (+ extend) already existing implementations.
 
 This project is intended to be a collaborative project of the scientific community and the contribution of EOF variants in the form of pull requests is explicitly encouraged.
 If you are interested, just `contact me`_ or open an `Issue`_.
@@ -112,12 +131,14 @@ Documentation_ is work in progress. Meanwhile check out some examples_ to get st
 + Rotated_ EOF analysis (Varimax, Promax)
 + Weighted_ EOF analysis
 + Multivariate_ EOF analysis
-
-.. _T-mode: https://xeofs.readthedocs.io/en/latest/auto_examples/1uni/plot_eof-tmode.html#sphx-glr-auto-examples-1uni-plot-eof-tmode-py
-.. _S-mode: https://xeofs.readthedocs.io/en/latest/auto_examples/1uni/plot_eof-smode.html#sphx-glr-auto-examples-1uni-plot-eof-smode-py
-.. _Weighted: https://xeofs.readthedocs.io/en/latest/auto_examples/1uni/plot_weighted_eof.html#sphx-glr-auto-examples-1uni-plot-weighted-eof-py
-.. _Rotated: https://xeofs.readthedocs.io/en/latest/auto_examples/1uni/plot_rotated_eof.html#sphx-glr-auto-examples-1uni-plot-rotated-eof-py
-.. _Multivariate: https://xeofs.readthedocs.io/en/latest/auto_examples/1uni/plot_multivariate-eof-analysis.html#sphx-glr-auto-examples-1uni-plot-multivariate-eof-analysis-py
++ Significance analysis via bootstrapping
++ Maximum Covariance Analysis
+
+.. _T-mode: https://xeofs.readthedocs.io/en/latest/auto_examples/1eof/plot_eof-tmode.html#sphx-glr-auto-examples-1eof-plot-eof-tmode-py
+.. _S-mode: https://xeofs.readthedocs.io/en/latest/auto_examples/1eof/plot_eof-smode.html#sphx-glr-auto-examples-1eof-plot-eof-smode-py
+.. _Weighted: https://xeofs.readthedocs.io/en/latest/auto_examples/1eof/plot_weighted_eof.html#sphx-glr-auto-examples-1eof-plot-weighted-eof-py
+.. _Rotated: https://xeofs.readthedocs.io/en/latest/auto_examples/1eof/plot_rotated_eof.html#sphx-glr-auto-examples-1eof-plot-rotated-eof-py
+.. _Multivariate: https://xeofs.readthedocs.io/en/latest/auto_examples/1eof/plot_multivariate-eof-analysis.html#sphx-glr-auto-examples-1eof-plot-multivariate-eof-analysis-py
 .. _Documentation: https://xeofs.readthedocs.io/en/latest/
 .. _examples: https://xeofs.readthedocs.io/en/latest/auto_examples/index.html
 
@@ -128,6 +149,7 @@ Credits
 
 - Project folder structure: yngvem_
 - Testing data: xarray_ \& pooch_
+- All developers of the EOF packages mentioned above
 
 
 .. _NumPy: https://www.numpy.org

docs/_autosummary/xeofs.models.Bootstrapper.rst

@@ -0,0 +1,31 @@
+xeofs.models.Bootstrapper
+=========================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: Bootstrapper
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~Bootstrapper.__init__
+ ~Bootstrapper.bootstrap
+ ~Bootstrapper.eofs
+ ~Bootstrapper.explained_variance
+ ~Bootstrapper.get_params
+ ~Bootstrapper.n_significant_modes
+ ~Bootstrapper.pcs
+
+
+
+
+
+

docs/_autosummary/xeofs.models.EOF.rst

@@ -0,0 +1,34 @@
+xeofs.models.EOF
+================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: EOF
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~EOF.__init__
+ ~EOF.eofs
+ ~EOF.eofs_as_correlation
+ ~EOF.explained_variance
+ ~EOF.explained_variance_ratio
+ ~EOF.pcs
+ ~EOF.project_onto_eofs
+ ~EOF.reconstruct_X
+ ~EOF.singular_values
+ ~EOF.solve
+
+
+
+
+
+

docs/_autosummary/xeofs.models.MCA.rst

@@ -0,0 +1,36 @@
+xeofs.models.MCA
+================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: MCA
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~MCA.__init__
+ ~MCA.explained_covariance
+ ~MCA.heterogeneous_patterns
+ ~MCA.homogeneous_patterns
+ ~MCA.pcs
+ ~MCA.project_onto_left_singular_vectors
+ ~MCA.project_onto_right_singular_vectors
+ ~MCA.reconstruct_XY
+ ~MCA.singular_values
+ ~MCA.singular_vectors
+ ~MCA.solve
+ ~MCA.squared_covariance_fraction
+
+
+
+
+
+

docs/_autosummary/xeofs.models.Rotator.rst

@@ -0,0 +1,32 @@
+xeofs.models.Rotator
+====================
+
+.. currentmodule:: xeofs.models
+
+.. autoclass:: Rotator
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~Rotator.__init__
+ ~Rotator.eofs
+ ~Rotator.eofs_as_correlation
+ ~Rotator.explained_variance
+ ~Rotator.explained_variance_ratio
+ ~Rotator.pcs
+ ~Rotator.project_onto_eofs
+ ~Rotator.reconstruct_X
+
+
+
+
+
+

docs/_autosummary/xeofs.models.rotator.Rotator.rst

@@ -0,0 +1,32 @@
+xeofs.models.rotator.Rotator
+============================
+
+.. currentmodule:: xeofs.models.rotator
+
+.. autoclass:: Rotator
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~Rotator.__init__
+ ~Rotator.eofs
+ ~Rotator.eofs_as_correlation
+ ~Rotator.explained_variance
+ ~Rotator.explained_variance_ratio
+ ~Rotator.pcs
+ ~Rotator.project_onto_eofs
+ ~Rotator.reconstruct_X
+
+
+
+
+
+

docs/_autosummary/xeofs.pandas.Bootstrapper.rst

@@ -0,0 +1,31 @@
+xeofs.pandas.Bootstrapper
+=========================
+
+.. currentmodule:: xeofs.pandas
+
+.. autoclass:: Bootstrapper
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~Bootstrapper.__init__
+ ~Bootstrapper.bootstrap
+ ~Bootstrapper.eofs
+ ~Bootstrapper.explained_variance
+ ~Bootstrapper.get_params
+ ~Bootstrapper.n_significant_modes
+ ~Bootstrapper.pcs
+
+
+
+
+
+

docs/_autosummary/xeofs.pandas.EOF.rst

@@ -0,0 +1,34 @@
+xeofs.pandas.EOF
+================
+
+.. currentmodule:: xeofs.pandas
+
+.. autoclass:: EOF
+ :members:
+ :show-inheritance: 
+ :inherited-members:
+
+
+ .. automethod:: __init__
+
+
+ .. rubric:: Methods
+
+ .. autosummary::
+
+ ~EOF.__init__
+ ~EOF.eofs
+ ~EOF.eofs_as_correlation
+ ~EOF.explained_variance
+ ~EOF.explained_variance_ratio
+ ~EOF.pcs
+ ~EOF.project_onto_eofs
+ ~EOF.reconstruct_X
+ ~EOF.singular_values
+ ~EOF.solve
+
+
+
+
+
+