Question on R GIS packages to extract point associations

Hi all,

Eons ago Hawthorne Beyer had Hawths Tools that used R to provide some 
really useful things like split shape files such as the IUCN or Mammals 
of the World into species specific files.? This has long since been 
defunct >15 years.? I do not recall but I think there was also an 
association module that was able to extract polygon overlay features 
related to the point data.

I can accomplish what I am interested in using ESRI ArcGIS or ArcPro but 
it takes a lot of time to set this up. Then run this one species at a 
time using Xtools.

What I need to do is extract species associations (point data) from 
multiple layers of shape file polygons that are varied ecological 
attributes.
This extracts all of the attributes of the overlays for each point layer.
Examples are elevation, vegetation types, ecosystem etc. then write the 
table of all associations by species.
Often I need to include proximity to water bodies like rivers, lakes and 
lagoons.

Are/Is there an R package or packages that can do this w/o loading the 
GIS and using the point data and ecological attribute polygons using R?

I have hundreds of species I need to do this with at varied geographic 
levels, both country level and landscape level like Mesoamerica, 
Caribbean etc.

Thanks to any R GIS gurus other there for a reply.

Bruce Miller