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I'm looking for appropriate types of analysis for a data set that contains counts of different crab species across 4 sites with 3 replicates per site (12 in total) over a time period of 1.5 years - 5 sampling time points.

The peculiarity of the data set is that each crab species only occurs on specific coral hosts. I'm thus following their hosts throughout time. A brief example: Colony 1 has a single crab at t1, two crabs at t2, and no crabs at t3, whereas Colony 2 has three crabs t1, t2 and t3. This would indicate that the crab abundance in colony 1 fluctuates much more. Currently, I have about 50 Colonies per site, so 200 in total. I'm interested to see how crab abundance on these colonies changes over time depending on the sites and also which impact the coral host species has. For instance: Does the abundance of crabs on coral species "Pavona" fluctuate more than abundance of crabs on coral species "Pocillopora"?

In summary, I would like to analyse this data regarding general changes in community composition of crabs over time and across sites but, more specifically, also to follow each colony through time and then compare this data to see whether certain coral species are prone to be colonized/abandoned more frequently than others.

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I'd recommend using the Temporal BetaDiversity Index (TBI) from Legendre available at the R package adespatial. You would only need a species composition matrix replicated in time. The stimodel function of adespatial could also be useful for testing interaction between time and space in species composition.

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  • $\begingroup$ Thank you! I will have a look at it. I also read about analysis like turnover analysis. I'm specifically interested in identifying "gains" and "losses" of crabs on each colony through time and how they differ between different species of corals. Is there ways to compare this too? Maybe I have to explain better: Each coral species contains one species of crab. I would like to compare how the different colony/crab pairings perform (gains/losses), so community composition is perhaps not the overarching theme. $\endgroup$ Commented Apr 12, 2023 at 14:53

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