I collected benthic samples from 12 stations (3 samples per station across 4 locations) across mudflats from one estuary, in autumn & the following spring, totalling 72 samples. In addition, I collected one sediment core from each station per season (total 24). 

Data analysis is being conducted through R, though I do have access to CAP4. Within R, I've generated dendrograms, NMDS plots, rarefaction curves and basic Simpson's diversity analysis (Vegan package).

Sediment analysis was conducted through Gradistat.

To understand benthic density/presence on sediment type, I'm trying to analyse sediment composition against benthos for each station/season.  I'm assuming it is better to analyse against the full breakdown of sediment type rather than the generated classification (i.e. muddy sand/sandy mud).

However, to get this working in R, there is a lot of data that would need to be imputed into the main data sheet alongside the species/site data and I'm really not sure the best way to do this/how it would look. 

Additionally, I also not too sure what package/analysis is the best to use to analyse these data?

Any help or advice would be greatly appreciated.