Hi, Seham.

The works of Aoife Gowen could be helpful.

Check:

Article NIR Hyperspectral Image analysis using R. Part 1: Introduction

Article NIR Hyperspectral Image analysis using R. Part 2: working wi...

Article NIR Hyperspectral Image analysis using R. Part 3: rudimentar...

Article NIR hyperspectral image analysis using R. Part 4: Pre-treatm...

Article Near Infrared Hyperspectral Image Analysis Using R. Part 6: ...

Try here:

http://hyperspec.r-forge.r-project.org/

If you have values of water content then you try to do a regression analysis, such as PLSR.

hello Seham

this may help you https://www.r-bloggers.com/computing-and-visualizing-pca-in-r/