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 two R packages (ReplicatedPointPatterns and RSPPlme4). The packages are still in development but if you are interested in testing it out on your data, here and here are links to the source code on GitHub. RSPPlme4 is faster, more user friendly and with better help files, and should be used unless you have specific reasons for using ReplicatedPointPatterns (e.g. you are interested in controlling for a continuous correlation structure).
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:
It took me a little effort to get this 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
There will undoubtedly be bugs so use with care, especially when doing something new! 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.