Как сравнить индекс Шеннона между ручьями с разной обработкой (не выпасаемые и не выпасаемые)?

Question

      Here are my data:
A) 9 different creeks. 
B) 3 different treatments (Intensively grazed, Extensively grazed, Ungrazed)
C) Sampling: fish, insects, "crabs & shrimp" (let's call this group shellfish) and benthos
D) There are 3 creeks for each treatment.
E) All samples are from one event. 
      a) Fish (one catch/creek). 
      b) Insects (6 traps/creek). 
      c) Shellfish (one catch/creek). 
      d) Benthos (3 samples/creek)

I want to examine if the treatment influences the diversity for each sampled group as for the totality of all groups. I want to use the Shannon Diversity Index, abundance and richness. 

What steps should I follow in R to accomplish this? I would really appreciate a step-by-step approach since I am very new to R. 

Thank you for any imput!!!

Пока знаю только, что мне понадобится пакет "БиоразнообразиеR". Мне нужна пошаговая инструкция.