We describe methods to analyze replicated point patterns in ecology in a recent paper (Bagchi & Illian, 2015). To facilitate use of these methods by ecologists, I have written an R package (ReplicatedPointPatterns). The package is still very much in development but if you are interested in testing it out on your data, here is a link to the source code on GitHub.
To use it you will need to compile it for your system. If you are using a system set up to use git then that is quite easy, just install the devtools package from CRAN and then do:
I’ve tried this successfully on computers running both Ubuntu 15.4 and Windows 7. It took me a little effort to get working on Windows due to some problems getting devtools installed. This might help you with getting set up: http://r-pkgs.had.co.nz/git.html
The help pages are still very rudimentary and there will undoubtedly be major bugs so use with care! If you have questions, please get in touch. I’m also happy to collaborate on using these techniques, so if you feel like your analyses will benefit from having me on-board drop me a line and we can go from there.