Metadata-Version: 2.1
Name: xeofs
Version: 2.2.2
Summary: Comprehensive EOF analysis in Python with xarray: A versatile, multidimensional, and scalable tool for advanced climate data analysis
Home-page: https://github.com/nicrie/xeofs
License: MIT
Author: Niclas Rieger
Author-email: niclasrieger@gmail.com
Requires-Python: >=3.10,<3.12
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: dask (>=2023.0.1)
Requires-Dist: netCDF4 (>=1.5.7,<2.0.0)
Requires-Dist: numba (>=0.57,<0.58)
Requires-Dist: numpy (>=1.24,<1.25)
Requires-Dist: pandas (>=1.4.1)
Requires-Dist: poetry (>=1.6,<2.0)
Requires-Dist: pooch (>=1.6.0,<2.0.0)
Requires-Dist: scikit-learn (>=1.0.2)
Requires-Dist: statsmodels (>=0.14.0)
Requires-Dist: tqdm (>=4.64.0,<5.0.0)
Requires-Dist: typing-extensions (>=4.8.0,<5.0.0)
Requires-Dist: xarray (>=0.21.1)
Requires-Dist: xarray-datatree (>=0.0.5)
Requires-Dist: zarr (>=2.0.0)
Project-URL: Documentation, https://xeofs.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/nicrie/xeofs
Description-Content-Type: text/markdown

![xeofs logo](docs/logos/xeofs_logo.png)

| Versions                   | ![PyPI](https://img.shields.io/pypi/v/xeofs) ![Conda](https://img.shields.io/conda/vn/conda-forge/xeofs) |
|----------------------------|:---------------------------------------------------------------------------------------------:|
| Build & Testing            | ![Build](https://img.shields.io/github/actions/workflow/status/nicrie/xeofs/ci.yml?branch=main) ![Coverage](https://codecov.io/gh/nicrie/xeofs/branch/main/graph/badge.svg?token=8040ZDH6U7) |
| Code Quality               | ![Black](https://img.shields.io/badge/code%20style-black-000000.svg)                           |
| Documentation              | ![Docs](https://readthedocs.org/projects/xeofs/badge/?version=latest)                          |
| Citation & Licensing       | ![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.6323012.svg) ![License](https://img.shields.io/pypi/l/xeofs) |
| User Engagement            | ![Downloads](https://img.shields.io/pypi/dw/xeofs) [![All Contributors](https://img.shields.io/github/all-contributors/nicrie/xeofs?color=ee8449&style=flat-square)](#contributors)                                            |

## Overview

`xeofs` is a dedicated Python package for dimensionality reduction in the realm of climate science, offering methods like PCA, known as EOF analysis within the field, and related variants. Seamlessly integrated with `xarray` and `Dask`, it's tailored for easy handling and scalable computation on large, multi-dimensional datasets, making advanced climate data analysis both accessible and efficient.

- **Multi-Dimensional**: Designed for `xarray` objects, it applies dimensionality reduction to multi-dimensional data while maintaining data labels.
- **Dask-Integrated**: Supports large datasets via `Dask` xarray objects
- **Extensive Methods**: Offers various dimensionality reduction techniques
- **Adaptable Output**: Provides output corresponding to the type of input, whether single or list of `xr.DataArray` or `xr.Dataset`
- **Missing Values**: Handles `NaN` values within the data
- **Bootstrapping**: Comes with a user-friendly interface for model evaluation using bootstrapping
- **Efficient**: Ensures computational efficiency, particularly with large datasets through randomized SVD
- **Modular**: Allows users to implement and incorporate new dimensionality reduction methods

## Installation

To install the package, use either of the following commands:

```bash
conda install -c conda-forge xeofs
```

or

```bash
pip install xeofs
```

## Quickstart

In order to get started with `xeofs`, follow these simple steps:

**Import the package**
    
```python
import xeofs as xe
```

**EOF analysis**

```python
model = xe.models.EOF(n_modes=10)
model.fit(data, dim="time")
comps = model.components()  # EOFs (spatial patterns)
scores = model.scores()  # PCs (temporal patterns)
```

**Varimax-rotated EOF analysis**

```python
rotator = xe.models.EOFRotator(n_modes=10)
rotator.fit(model)
rot_comps = rotator.components()  # Rotated EOFs (spatial patterns)
rot_scores = rotator.scores()  # Rotated PCs (temporal patterns)
```

**Maximum Covariance Analysis (MCA)**

```python
model = xe.models.MCA(n_modes=10)
model.fit(data1, data2, dim="time")
comps1, comps2 = model.components()  # Singular vectors (spatial patterns)
scores1, scores2 = model.scores()  # Expansion coefficients (temporal patterns)
```

**Varimax-rotated MCA**

```python
rotator = xe.models.MCARotator(n_modes=10)
rotator.fit(model)
rot_comps = rotator.components()  # Rotated singular vectors (spatial patterns)
rot_scores = rotator.scores()  # Rotated expansion coefficients (temporal patterns)
```

To further explore the capabilities of `xeofs`, check out the [available documentation](https://xeofs.readthedocs.io/en/latest/) and [examples](https://xeofs.readthedocs.io/en/latest/auto_examples/index.html).
For a full list of currently available methods, see the [Reference API](https://xeofs.readthedocs.io/en/latest/api.html).

## Documentation

For a more comprehensive overview and usage examples, visit the [documentation](https://xeofs.readthedocs.io/en/latest/).

## Contributing

Contributions are highly welcomed and appreciated. If you're interested in improving `xeofs` or fixing issues, please read our [Contributing Guide](https://xeofs.readthedocs.io/en/latest/overview_3)

## License

This project is licensed under the terms of the [MIT license](https://github.com/nicrie/xeofs/blob/main/LICENSE).

## Contact

For questions or support, please open a [Github issue](https://github.com/nicrie/xeofs/issues).

## Credits

- Randomized PCA: [scikit-learn](https://scikit-learn.org/stable/)
- EOF analysis: Python package [eofs](https://github.com/ajdawson/eofs) by Andrew Dawson
- MCA: Python package [xMCA](https://github.com/Yefee/xMCA) by Yefee
- CCA: Python package [CCA-Zoo](https://github.com/jameschapman19/cca_zoo) by James Chapman
- ROCK-PCA: Matlab implementation by [Diego Bueso](https://github.com/DiegoBueso/ROCK-PCA)

## How to cite?

When using `xeofs`, kindly remember to cite the original references of the methods employed in your work. Additionally, if `xeofs` is proving useful in your research, we'd appreciate if you could acknowledge its use with the following citation:

```bibtex
@software{rieger_xeofs_2023,
title = {xeofs: Comprehensive EOF analysis in Python with xarray: A versatile, multidimensional, and scalable tool for advanced climate data analysis},
url = {https://github.com/nicrie/xeofs}
version = {x.y.z},
author = {Rieger, N. and Levang, S. J.},
date = {2023},
doi = {10.5281/zenodo.6323011}
```

## Contributors

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