olivertomic / Hoggorm
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hoggorm
.. image:: https://img.shields.io/pypi/l/hoggorm.svg :target: https://github.com/olivertomic/hoggorm/blob/master/LICENSE
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hoggorm is a Python package for explorative multivariate statistics in Python. It contains the following methods:
-
PCA (principal component analysis)
-
PCR (principal component regression)
-
PLSR (partial least squares regression)
- PLSR1 for single variable responses
- PLSR2 for multivariate responses
-
matrix correlation coefficients RV, RV2 and SMI.
Unlike scikit-learn
, which is an excellent python machine learning package focusing on classification, regression, clustering and predicition, hoggorm rather aims at understanding and interpretation of the variance in the data. hoggorm also contains tools for prediction.
The complementary package hoggormplot
can be used for visualization of results of models trained with hoggorm.
.. _scikit-learn: https://scikit-learn.org/stable/ .. _hoggormplot: https://github.com/olivertomic/hoggormPlot
Examples
.. |ColabCancer| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/olivertomic/hoggorm/blob/master/examples/PCA/PCA_on_cancer_data.ipynb :alt: Open in Colab
.. |BinderCancer| image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/olivertomic/hoggorm/master?filepath=examples/PCA/PCA_on_cancer_data.ipynb :alt: Open in Binder
.. |BinderSensory| image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/olivertomic/hoggorm/master?filepath=examples%2FPCR%2FPCR_on_sensory_and_fluorescence_data.ipynb :alt: Open in Binder
.. |ColabSensory| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/olivertomic/hoggorm/blob/master/examples/RV_%26_RV2/RV_and_RV2_on_sensory_and_fluorescence_data.ipynb :alt: Open In Colab
.. |ColabPCRCheese| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/olivertomic/hoggorm/blob/master/examples/PCR/PCR_on_sensory_and_fluorescence_data.ipynb :alt: Open In Colab
.. |ColabPLSR2Cheese| image:: https://colab.research.google.com/assets/colab-badge.svg :target: https://colab.research.google.com/github/olivertomic/hoggorm/blob/master/examples/PLSR/PLSR_on_sensory_and_fluorescence_data.ipynb :alt: Open In Colab
Below are links to some Jupyter notebooks that illustrate how to use hoggorm and hoggormplot with the methods mentioned above. All examples are also found in the examples
_ folder.
-
Jupyter notebooks with examples of how to use hoggorm
- for
PCA
_ -PCA on cancer data
_ on men in OECD countries |ColabCancer| |BinderCancer| -PCA on NIR spectroscopy data
_ measured on gasoline -PCA on sensory data
_ measured on cheese - for
PCR
_ -PCR on sensory and fluorescence spectroscopy data
_ measured on cheese |ColabPCRCheese| - for
PLSR1
_ for univariate response (one response variable) -PLSR1 on NIR spectroscopy and octane data
_ measured on gasoline - for
PLSR2
_ for multivariate response (multiple response variables) -PLSR2 on sensory and fluorescence spectroscopy data
_ measured on cheese |ColabPLSR2Cheese| - for matrix correlation coefficients
RV and RV2
_ -RV and RV2 coefficient on sensory and fluorescence spectroscopy data
_ measured on cheese |ColabSensory| |BinderSensory| - for the
SMI
_ (similarity of matrix index) -SMI on sensory data and fluorescence data
_ -SMI on pseudo-random numbers
_
- for
.. _examples: https://github.com/olivertomic/hoggorm/tree/master/examples .. _PCA: https://github.com/olivertomic/hoggorm/tree/master/examples/PCA .. _PCR: https://github.com/olivertomic/hoggorm/tree/master/examples/PCR .. _PLSR1: https://github.com/olivertomic/hoggorm/tree/master/examples/PLSR .. _PLSR2: https://github.com/olivertomic/hoggorm/tree/master/examples/PLSR .. _RV and RV2: https://github.com/olivertomic/hoggorm/tree/master/examples/RV_%26_RV2 .. _PCA on cancer data: https://github.com/olivertomic/hoggorm/blob/master/examples/PCA/PCA_on_cancer_data.ipynb .. _PCA on NIR spectroscopy data: https://github.com/olivertomic/hoggorm/blob/master/examples/PCA/PCA_on_spectroscopy_data.ipynb .. _PCA on sensory data: https://github.com/olivertomic/hoggorm/blob/master/examples/PCA/PCA_on_descriptive_sensory_analysis_data.ipynb .. _PCR on sensory and fluorescence spectroscopy data: https://github.com/olivertomic/hoggorm/blob/master/examples/PCR/PCR_on_sensory_and_fluorescence_data.ipynb .. _PLSR1 on NIR spectroscopy and octane data: https://github.com/olivertomic/hoggorm/blob/master/examples/PLSR/PLSR_on_NIR_and_octane_data.ipynb .. _PLSR2 on sensory and fluorescence spectroscopy data: https://github.com/olivertomic/hoggorm/blob/master/examples/PLSR/PLSR_on_sensory_and_fluorescence_data.ipynb .. _RV and RV2 coefficient on sensory and fluorescence spectroscopy data: https://github.com/olivertomic/hoggorm/blob/master/examples/RV_%26_RV2/RV_and_RV2_on_sensory_and_fluorescence_data.ipynb .. _SMI: https://github.com/olivertomic/hoggorm/tree/master/examples/SMI .. _SMI on sensory data and fluorescence data: https://github.com/olivertomic/hoggorm/blob/master/examples/SMI/SMI_on_sensory_and_fluorescence.ipynb .. _SMI on pseudo-random numbers: https://github.com/olivertomic/hoggorm/blob/master/examples/SMI/SMI_pseudo-random_numbers.ipynb
Requirements
Make sure that Python 3.5 or higher is installed. A convenient way to install Python and many useful packages for scientific computing is to use the Anaconda distribution
_.
.. _Anaconda distribution: https://www.anaconda.com/download/
- numpy >= 1.9
Installation
Using pip
.. image:: https://pepy.tech/badge/hoggorm :target: https://pepy.tech/project/hoggorm :alt: PyPI Downloads
.. image:: https://pepy.tech/badge/hoggorm/month :target: https://pepy.tech/project/hoggorm/month :alt: PyPI Downloads
.. image:: https://pepy.tech/badge/hoggorm/week :target: https://pepy.tech/project/hoggorm/week :alt: PyPI Downloads
Install hoggorm easily from the command line from the PyPI - the Python Packaging Index
_.
.. _PyPI - the Python Packaging Index: https://pypi.python.org/pypi
.. code-block:: bash
pip install hoggorm
Using conda
.. image:: https://img.shields.io/conda/dn/conda-forge/hoggorm.svg :target: https://anaconda.org/conda-forge/hoggorm :alt: Conda Downloads
.. image:: https://img.shields.io/conda/vn/conda-forge/hoggorm.svg :target: https://anaconda.org/conda-forge/hoggorm :alt: Conda Version
You can install using the conda package manager by running
.. code-block:: bash
conda install -c conda-forge hoggorm
Documentation
.. image:: https://readthedocs.org/projects/hoggorm/badge/?version=latest
- Documentation at
Read the Docs
_ - Jupyter notebooks with
examples
_ of how to use Hoggorm together with the complementary plotting packagehoggormplot
_.
.. _Read the Docs: https://hoggorm.readthedocs.io/en/latest/ .. _examples: https://github.com/olivertomic/hoggorm/tree/master/examples .. _hoggormplot: https://github.com/olivertomic/hoggormPlot
Citing hoggorm
If you use hoggorm in a report or scientific publication, we would appreciate citations to the following paper:
.. image:: https://joss.theoj.org/papers/10.21105/joss.00980/status.svg :target: https://doi.org/10.21105/joss.00980
Tomic et al., (2019). hoggorm: a python library for explorative multivariate statistics. Journal of Open Source Software, 4(39), 980, https://doi.org/10.21105/joss.00980
Bibtex entry:
.. code-block:: bash
@article{hoggorm,
title={hoggorm: a python library for explorative multivariate statistics},
author={Tomic, Oliver and Graff, Thomas and Liland, Kristian Hovde and N{\ae}s, Tormod},
journal={The Journal of Open Source Software},
volume={4},
number={39},
year={2019},
doi={10.21105/joss.00980},
url={http://joss.theoj.org/papers/10.21105/joss.00980}
}