I am just reviewing Fresnel's equations where Reflectance $R$ is equal to
where $r$ is the complex reflection coefficient. Is there an equation that relates $R$ to intensity or is there a reason one is related to the other?
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If the authors plot intensity rather than reflectance, it's probably because the absolute reflectance is not of interest to the study at hand. The interest could me more focused on the location in wavelength of features such as peaks and valleys. The interest is to extract information about the system from the wavelengths.
Absolute reflectance is difficult to measure. Intensity is considerably easier. Reflectance requires a calibrated detector system, or a known reference sample, or both. Even then, the measurement requires quite a bit of care. If the absolute reflectance is of little interest, there is little incentive to measure it. Spectroscopy more often than not is about the location of features.
On the other hand, if the location of features must be known to a high degree of accuracy, absolute measurements might be required, because non-uniform spectral response of a detector can introduce small errors in the position of peaks.