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I have an experiment that investigates the affects of small mammal presence (present or absent) and fire (burned or unburned) in a replicated full factorial block design (4 plots--each treatment combo = 1 block). There are 4 transect lines with 12-(25cmx50cm) quadrats that I count the plants that grow in each treatment plot, giving 48 quadrats per treatment per block. And there are 5 blocks. I have taken these measurements for 4 years.

There are two dominant plant species that have partitioned into what I believe is a neat spatial relationship where they don't share the same space. And because all of the statistics I am familiar with require spatial independence I am not sure what to do.

How can I analyze the spatial relationship between these two species and whether or not it is true that they have niche partitioned. Normally I have averaged together the density counts for each treatment plot and run a lme with BLOCK as a random factor

Is there a way to show the change over time in the spatial relationship? I am ok with investigating just one year (the last year seems to be the peak counts that we have gotten for both species and when I really noticed the space partitioning)

Thanks!

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