I am working in the Sahel on agroforestry parklands where there is a strong interaction between crops and animals in pasture. The animal brings manure to the soil and the crops produce fodder.
First we need to define the evaluation parameters which could serve as metrics for evaluation. For example, soil organic carbon (soil health) could be one metric, crop fodder yield could be another, soil microbial health, nutrient recycling and so on. These metrics could be aligned with the overall objective of your research or experiment. The complexity of the width and depth of the metrics depends on your objectives.
The integration of the animal and plant systems are illustrated in a system of grazing. The critical issue is the pasturing at such a way that perennial roots are not eliminated so the system can be sustained. The ability to do this has depended on rotation intensive grazing with sufficient recovery to keep the root systems intact. Alternatively the forage can be taken to animals with the issue of repatriating the manures back to the fields they originated. Crop systems can be rotated with animal grazing system which reduces both animal and plant diseases and improves both plant and animal health. The ability to have long term system studies should be abie to use Carbon, Nitrogen and the levels of biological measures as chemical and biological measurements. The assessment of physical attributes of the soil are also very indicative of either degeneration, sustainability or regeneration in the systems. Extended controlled work is needed to best analyze these effects.
@Moussa, in addition to suggestions above you may also consider chemical and structural improvement of soil, soil stability and erosion control, crop diversity, micro-climate improvement, microbial and beneficial enzyme activities, shelter habitat for wildlife and economics as an indicator.
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