R vegan - what are 'species' and 'sites'

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I'm trying to perform RDA in R, using the package vegan and, well, it's getting a bit confusing. This is quite tricky to explain, but hopefully I make some sense...

The vegan package is developed for ecological data. Because of that it seems to use 'sites' and 'species' as specific named terms/factors in the model?

This is confusing as some datasets (e.g. Iris) have columns named 'species' for example.

I do not have sites, nor species. I have plots IDs, each plot has been applied fertiliser (characterised by 5 independent variables) and for each plot plant nutrition has been analysed (6 dependent variables).

I don't quite understand exactly what "species" and "site" are referring to within Vegan. For example, at this link: https://rstudio-pubs-static.s3.amazonaws.com/259028_dbe846c67e144065b4c2bcd012fb130d.html

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Sorry for the ignorance, this is one package I've struggled with. Previously, I've done plenty of PCAs using prcomp and GGFortify, but it appears there isn't an equivalent route for RDA.

vegan r
1 Answers

Sites are the samples (the things which are measured e.g the plots in your case) and species are properties or features of the samples. A biplot shows both how features are different and how samples are different. For display='sites', site data is used directly for the axes and the species are just being drawn relatively to them. So it's just to set your perspective.

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