Smelly rats

Replicating - or trying to replicate - a paper[1] about classifying rats which have different onion diets.

Description

The paper uses H+ NMR spectra taken from the urine of rats which have different levels of onion in their diet. The goal is to classify the diet of the rat with the spectral data.

These repository implements a couple of the applied analysis in Python:

• HNMR spectra per diet: Implements the average HNMR spectra per dietary group.
• interval partial least squares Implements interval partial least squares to find the spectral bands with which the dietary groups can be classified most correctly.
• PCA: Applies PCA to the spectra to look for separation of the dietary groups in lower dimensional space.
• Resampling spectral bands: Implements a resample method which works on pandas.FloatIndex and works similar as the resample method for pd.DateTimeIndex - useful to reduce the resolution of the spectral bands.

Requirements

Python 3 and see here.

Data

The data can be found here.

Sources

[1] H. Winning, E. Roldán‐Marín, L.O. Dragsted, N. Viereck, M. Poulsen, C. Sánchez‐Moreno, M.P. Cano, S.B. Engelsen, An exploratory NMR nutri-metabonomic investigation reveals dimethyl sulfone as a dietary biomarker for onion intake, Analyst 2009, 134 (11) 2344-2351