Hello
I have run the tutorial on gneiss and been trying to do the analysis on my own dataset, but got some basic questions about this analysis, as I don't fully understand it.
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I am not sure I fully understand what question this analysis is trying to answer. I thought it was testing which of the factors of interest influence the relative abundance of species in samples. So essentially it's like running a multiple regression?
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Following up on the previous question, what is the null hypothesis?
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I guess the main chunk of the analysis is a multiple regression. However, there are no p-values/F-scores/degrees of freedom, so how does one know which variable to keep in the model and which to omit? Also, what test statistics would you one quote in a paper?
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How does one interpret the prediction and residual plots? I don't really understand the relevance of a scatter plot between the first two balances, and then what I should expect to see in those plots. Also, what do the percentages in brackets represent?
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Finally, is the tree presented in the analysis representative of how the taxa are phylogenetically connected?
Thanks