[R-sig-Geo] Newbie questions

[quantrum75]

Hello all,I am an absolute newbie to spatial statistics, but I am quite thoroughly obsessed by it currently. I am an engineer by training, so I can find my way around math and programming. I have begun to look at the Spatial CRAN view and am absolutely blown away by the enormous body of work in there. So thank you all for that. But I am equally confused regarding the right choice of software and statistical approach as well.
With that introduction, I will try to explain (one of) the problem(s) I am trying to solve. Of note, we absolutely do not deal with GIS issues.

We have a setup where we are trying to grow some bacterial cultures on a polygonal irregular surface. I am able to obtain 2-D projection views/images similar to the illustration attached to this mail. Some of the things I want to do are 

1) Establish a spatial statistical analytic pipeline to answer questions like
a) Are the patterns of bacterial island growth in different cultures statistically random or correlated?b) Are the distances from the boundary edge to a bacterial island random or have a pattern?

Now, the issue I have is, the bacterial islands have an "area", so I cannot really consider them as "point" processes. Yet, these "areas" are sufficiently far away from each other (relative to the polygonal boundary) that I can (to an approximation) consider them as being "point" processes (maybe?)...

Some of my questions are
1) Is it appropriate to use a "point processes" method or an "areal processes" method for analysis of this problem?
2) If point processes are ok, is it ok to weight the area and use the centroid at the location of the point?
3) Where do I start? I currently have 5 books - The Baddeley book (spatstat, for point processes), the Cressie book (for theory), the R-INLA book (Bayesian spatial statistics), Applied Spatial Analysis in R (Dr Bivand's book) and the Gelfand book (Hierarchical modelling)
4) Packages - Spatstat? sp? spdep? splancs? spatial? DCluster? AMOEBA? Which spatial regression package? Arghhhh.....
Now, I am not asking anyone to provide me with a ready made solution. I would simply appreciate if someone could point me in the right direction on how to start and go far from there. I am willing to learn and put in the necessary elbow grease to understand it well. Experts in spatial statistics are unavailable at my local college, so an immediate collaboration is bit far off. But something we can look into in the future.

Thank you for your kind consideration. Any and all advice is eagerly welcomed and I will be highly grateful for the same.RegardsQuant.
PS - Long term, I would like to contribute in some way to this group. If anyone is in need of any assistants for any packages, I am willing to volunteer my time.
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